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    On 9/11/2010 10:10 PM, hengame fallah wrote:

    <blockquote

      cite="mid:AANLkTincqkT-36smsyOibzB8=dkhiyJ14TB9FRrq_Mbh@mail.gmail.com"

      type="cite">This is .rtp for [PHE] in opls:<br>

    </blockquote>

    <br>

    ...wherein all the charge groups are neutral, unlike yours for BOC.

    This will be fairly moot for a PME simulation, however.<br>

    <br>

    <blockquote

      cite="mid:AANLkTincqkT-36smsyOibzB8=dkhiyJ14TB9FRrq_Mbh@mail.gmail.com"

      type="cite"><br>

      [ PHE ]<br>

      &nbsp;[ atoms ]<br>

      &nbsp;&nbsp;&nbsp;&nbsp; N&nbsp;&nbsp;&nbsp; opls_238&nbsp;&nbsp; -0.500&nbsp;&nbsp;&nbsp;&nbsp; 1<br>

      &nbsp;&nbsp;&nbsp;&nbsp; H&nbsp;&nbsp;&nbsp; opls_241&nbsp;&nbsp;&nbsp; 0.300&nbsp;&nbsp;&nbsp;&nbsp; 1<br>

      &nbsp;&nbsp;&nbsp; CA&nbsp;&nbsp;&nbsp; opls_224B&nbsp;&nbsp; 0.140&nbsp;&nbsp;&nbsp;&nbsp; 1<br>

      &nbsp;&nbsp;&nbsp; HA&nbsp;&nbsp;&nbsp; opls_140&nbsp;&nbsp;&nbsp; 0.060&nbsp;&nbsp;&nbsp;&nbsp; 1<br>

      &nbsp;&nbsp;&nbsp; CB&nbsp;&nbsp;&nbsp; opls_149&nbsp;&nbsp; -0.005&nbsp;&nbsp;&nbsp;&nbsp; 2<br>

      &nbsp;&nbsp; HB1&nbsp;&nbsp;&nbsp; opls_140&nbsp;&nbsp;&nbsp; 0.060&nbsp;&nbsp;&nbsp;&nbsp; 2<br>

      &nbsp;&nbsp; HB2&nbsp;&nbsp;&nbsp; opls_140&nbsp;&nbsp;&nbsp; 0.060&nbsp;&nbsp;&nbsp;&nbsp; 2<br>

      &nbsp;&nbsp;&nbsp;<span style="background-color: rgb(255, 255, 204);"> CG&nbsp;&nbsp;&nbsp;

        opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 2</span><br>

      &nbsp;&nbsp; CD1&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 3<br>

      &nbsp;&nbsp; HD1&nbsp;&nbsp;&nbsp; opls_146&nbsp;&nbsp;&nbsp; 0.115&nbsp;&nbsp;&nbsp;&nbsp; 3<br>

      &nbsp;&nbsp; CD2&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 4<br>

      &nbsp;&nbsp; HD2&nbsp;&nbsp;&nbsp; opls_146&nbsp;&nbsp;&nbsp; 0.115&nbsp;&nbsp;&nbsp;&nbsp; 4<br>

      &nbsp;&nbsp; CE1&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 5<br>

      &nbsp;&nbsp; HE1&nbsp;&nbsp;&nbsp; opls_146&nbsp;&nbsp;&nbsp; 0.115&nbsp;&nbsp;&nbsp;&nbsp; 5<br>

      &nbsp;&nbsp; CE2&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 6<br>

      &nbsp;&nbsp; HE2&nbsp;&nbsp;&nbsp; opls_146&nbsp;&nbsp;&nbsp; 0.115&nbsp;&nbsp;&nbsp;&nbsp; 6 <br>

      &nbsp;&nbsp;&nbsp; CZ&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 7 <br>

      &nbsp;&nbsp;&nbsp; HZ&nbsp;&nbsp;&nbsp; opls_146&nbsp;&nbsp;&nbsp; 0.115&nbsp;&nbsp;&nbsp;&nbsp; 7<br>

      &nbsp;&nbsp;&nbsp;&nbsp; C&nbsp;&nbsp;&nbsp; opls_235&nbsp;&nbsp;&nbsp; 0.500&nbsp;&nbsp;&nbsp;&nbsp; 8<br>

      &nbsp;&nbsp;&nbsp;&nbsp; O&nbsp;&nbsp;&nbsp; opls_236&nbsp;&nbsp; -0.500&nbsp;&nbsp;&nbsp;&nbsp; 8<br>

      &nbsp;[ bonds ]<br>

      &nbsp;&nbsp;&nbsp;&nbsp; N&nbsp;&nbsp;&nbsp;&nbsp; H<br>

      &nbsp;&nbsp;&nbsp;&nbsp; N&nbsp;&nbsp;&nbsp; CA<br>

      &nbsp;&nbsp;&nbsp; CA&nbsp;&nbsp;&nbsp; HA<br>

      &nbsp;&nbsp;&nbsp; CA&nbsp;&nbsp;&nbsp; CB<br>

      &nbsp;&nbsp;&nbsp; CA&nbsp;&nbsp;&nbsp;&nbsp; C<br>

      &nbsp;&nbsp;&nbsp; CB&nbsp;&nbsp; HB1<br>

      &nbsp;&nbsp;&nbsp; CB&nbsp;&nbsp; HB2<br>

      &nbsp;&nbsp;&nbsp; CB&nbsp;&nbsp;&nbsp; CG<br>

      &nbsp;&nbsp;&nbsp; CG&nbsp;&nbsp; CD1<br>

      &nbsp;&nbsp;&nbsp; CG&nbsp;&nbsp; CD2<br>

      &nbsp;&nbsp; CD1&nbsp;&nbsp; HD1<br>

      &nbsp;&nbsp; CD1&nbsp;&nbsp; CE1<br>

      &nbsp;&nbsp; CD2&nbsp;&nbsp; HD2<br>

      &nbsp;&nbsp; CD2&nbsp;&nbsp; CE2<br>

      &nbsp;&nbsp; CE1&nbsp;&nbsp; HE1<br>

      &nbsp;&nbsp; CE1&nbsp;&nbsp;&nbsp; CZ<br>

      &nbsp;&nbsp; CE2&nbsp;&nbsp; HE2<br>

      &nbsp;&nbsp; CE2&nbsp;&nbsp;&nbsp; CZ<br>

      &nbsp;&nbsp;&nbsp; CZ&nbsp;&nbsp;&nbsp; HZ<br>

      &nbsp;&nbsp;&nbsp;&nbsp; C&nbsp;&nbsp;&nbsp;&nbsp; O<br>

      &nbsp;&nbsp;&nbsp; -C&nbsp;&nbsp;&nbsp;&nbsp; N<br>

      <br>

      and i got the charges by Gaussian.<br>

    </blockquote>

    <br>

    Is your method suitable for OPLSAA charges? (I don't know). See

    <a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/How-tos/Parameterization">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>

    <br>

    Regarding the copy of all these files that you sent me off-list,

    please refrain from doing so unless somebody requests them. I gave

    you an itemized list of things to fix, and you haven't addressed any

    of them that I could see. I'll add another item to the list - your

    .hdb format is wrong for the *two* hydrogens you're still telling it

    to try to add to CB, which is causing the fatal error. However you

    have many others issues to address as well.<br>

    <br>

    You're doing something that is advanced - be prepared to read

    chapter 5 of the manual closely!<br>

    <br>

    Mark<br>

    <br>

    <blockquote

      cite="mid:AANLkTincqkT-36smsyOibzB8=dkhiyJ14TB9FRrq_Mbh@mail.gmail.com"

      type="cite">I'm very confused now <img goomoji="361"

        style="margin: 0pt 0.2ex; vertical-align: middle;"

        src="cid:part1.08040107.03060305@anu.edu.au"><br>

      <div class="gmail_quote">

        On Tue, Nov 9, 2010 at 2:13 PM, Mark Abraham <span dir="ltr">&lt;<a

            moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>&gt;</span>

        wrote:<br>

        <blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt

          0.8ex; border-left: 1px solid rgb(204, 204, 204);

          padding-left: 1ex;">

          <div text="#000000" bgcolor="#ffffff">

            <div>

              <div class="h5"> On 9/11/2010 9:09 PM, hengame fallah

                wrote:

                <blockquote type="cite">Dear Mark,<br>

                  <br>

                  I edited my pdb like this:<br>

                  ...<br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 41&nbsp; N&nbsp;&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -1.862&nbsp;&nbsp; 5.210&nbsp;&nbsp; 5.333

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 42&nbsp; H&nbsp;&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -2.325&nbsp;&nbsp; 4.344&nbsp;&nbsp; 5.618

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 43&nbsp; CA&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -1.001&nbsp;&nbsp; 5.232&nbsp;&nbsp; 4.169

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 44&nbsp; HA1 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.540&nbsp;&nbsp; 6.235&nbsp;&nbsp; 4.026<br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 45&nbsp; HA2 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.172&nbsp;&nbsp; 4.511&nbsp;&nbsp; 4.360

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 46&nbsp; CB&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -1.797&nbsp;&nbsp; 4.794&nbsp;&nbsp; 2.924

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 47&nbsp; HB1 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -2.244&nbsp;&nbsp; 3.809&nbsp;&nbsp; 3.204

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 48&nbsp; CG1 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -2.976&nbsp;&nbsp; 5.730&nbsp;&nbsp; 2.589<br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 49&nbsp; CD1 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -1.231&nbsp;&nbsp; 3.466&nbsp;&nbsp; 0.845

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 50&nbsp; HD1 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -2.070&nbsp;&nbsp; 2.790&nbsp;&nbsp; 1.081

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 51&nbsp; CD2 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.120&nbsp;&nbsp; 5.408&nbsp;&nbsp; 1.353

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 52&nbsp; HD2 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.357&nbsp;&nbsp; 6.277&nbsp;&nbsp; 1.986

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 53&nbsp; CE1 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.471&nbsp;&nbsp; 3.236&nbsp; -0.312

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 54&nbsp; HE1 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.717&nbsp;&nbsp; 2.381&nbsp; -0.964

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 55&nbsp; CE2 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.881&nbsp;&nbsp; 5.182&nbsp;&nbsp; 0.197

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 56&nbsp; HE2 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.706&nbsp;&nbsp; 5.870&nbsp; -0.054

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 57&nbsp; CZ&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.591&nbsp;&nbsp; 4.093&nbsp; -0.639<br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 58&nbsp; CG2 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.935&nbsp;&nbsp; 4.544&nbsp;&nbsp; 1.698<br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 59&nbsp; HG1 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -3.530&nbsp;&nbsp; 5.331&nbsp;&nbsp; 1.707

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 60&nbsp; HG2 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -3.708&nbsp;&nbsp; 5.729&nbsp;&nbsp; 3.431

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 61&nbsp; C&nbsp;&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -2.565&nbsp;&nbsp; 7.148&nbsp;&nbsp; 2.291

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 62&nbsp; O&nbsp;&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -2.716&nbsp;&nbsp; 8.035&nbsp;&nbsp; 3.131

                  <br>

                  ATOM&nbsp;&nbsp;&nbsp;&nbsp; 63&nbsp; Cl&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.525&nbsp;&nbsp; 3.816&nbsp; -2.062

                  <br>

                  END<br>

                  <br>

                  and my .rtp file for [ BOC ] is:<br>

                  <br>

                  <span style="background-color: rgb(102, 204, 204);">[

                    BOC ]</span><br>

                  &nbsp;<span style="background-color: rgb(255, 255, 153);">[

                    atoms ]</span><br>

                  &nbsp;&nbsp;&nbsp;&nbsp; N&nbsp;&nbsp;&nbsp; opls_238&nbsp;&nbsp; -0.500&nbsp;&nbsp;&nbsp;&nbsp; 1 <br>

                  &nbsp;&nbsp;&nbsp;&nbsp; H&nbsp;&nbsp;&nbsp; opls_241&nbsp;&nbsp;&nbsp; 0.300&nbsp;&nbsp;&nbsp;&nbsp; 1<br>

                  &nbsp;&nbsp;&nbsp; CA&nbsp;&nbsp;&nbsp; opls_224B&nbsp; -0.005&nbsp;&nbsp;&nbsp;&nbsp; 1<br>

                  &nbsp;&nbsp; HA1&nbsp;&nbsp;&nbsp; opls_140&nbsp;&nbsp;&nbsp; 0.060&nbsp;&nbsp;&nbsp;&nbsp; 1<br>

                  &nbsp;&nbsp; HA2&nbsp;&nbsp;&nbsp; opls_140&nbsp;&nbsp;&nbsp; 0.060&nbsp;&nbsp;&nbsp;&nbsp; 1<br>

                  &nbsp;&nbsp;&nbsp; CB&nbsp;&nbsp;&nbsp; opls_149&nbsp;&nbsp;&nbsp; 0.140&nbsp;&nbsp;&nbsp;&nbsp; 2<br>

                  &nbsp;&nbsp; HB1&nbsp;&nbsp;&nbsp; opls_140&nbsp;&nbsp;&nbsp; 0.060&nbsp;&nbsp;&nbsp;&nbsp; 2<br>

                  &nbsp;&nbsp; CG1&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 2<br>

                  &nbsp;&nbsp; CD1&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 3<br>

                  &nbsp;&nbsp; HD1&nbsp;&nbsp;&nbsp; opls_146&nbsp;&nbsp;&nbsp; 0.115&nbsp;&nbsp;&nbsp;&nbsp; 3<br>

                  &nbsp;&nbsp; CD2&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 4<br>

                  &nbsp;&nbsp; HD2&nbsp;&nbsp;&nbsp; opls_146&nbsp;&nbsp;&nbsp; 0.115&nbsp;&nbsp;&nbsp;&nbsp; 4<br>

                  &nbsp;&nbsp; CE1&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 5<br>

                  &nbsp;&nbsp; HE1&nbsp;&nbsp;&nbsp; opls_146&nbsp;&nbsp;&nbsp; 0.115&nbsp;&nbsp;&nbsp;&nbsp; 5<br>

                  &nbsp;&nbsp; CE2&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 6<br>

                  &nbsp;&nbsp; HE2&nbsp;&nbsp;&nbsp; opls_146&nbsp;&nbsp;&nbsp; 0.115&nbsp;&nbsp;&nbsp;&nbsp; 6 <br>

                  &nbsp;&nbsp;&nbsp; CZ&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp;&nbsp; 0.885&nbsp;&nbsp;&nbsp;&nbsp; 7<br>

                  &nbsp;&nbsp;&nbsp; Cl&nbsp;&nbsp;&nbsp; opls_264&nbsp;&nbsp; -1.000&nbsp;&nbsp;&nbsp;&nbsp; 7<br>

                  &nbsp;&nbsp; CG2&nbsp;&nbsp;&nbsp; opls_071&nbsp;&nbsp; -0.005&nbsp;&nbsp;&nbsp;&nbsp; 8<br>

                  &nbsp;&nbsp; HG1&nbsp;&nbsp;&nbsp; opls_140&nbsp;&nbsp;&nbsp; 0.060&nbsp;&nbsp;&nbsp;&nbsp; 8<br>

                  &nbsp;&nbsp; HG2&nbsp;&nbsp;&nbsp; opls_140&nbsp;&nbsp;&nbsp; 0.060&nbsp;&nbsp;&nbsp;&nbsp; 8<br>

                  &nbsp;&nbsp;&nbsp;&nbsp; C&nbsp;&nbsp;&nbsp; opls_235&nbsp;&nbsp;&nbsp; 0.700&nbsp;&nbsp;&nbsp;&nbsp; 9<br>

                  &nbsp;&nbsp;&nbsp;&nbsp; O&nbsp;&nbsp;&nbsp; opls_236&nbsp;&nbsp; -0.700&nbsp;&nbsp;&nbsp;&nbsp; 9<br>

                  &nbsp;<span style="background-color: rgb(255, 255, 153);">[

                    bonds ]</span><br>

                  &nbsp;&nbsp;&nbsp;&nbsp; N&nbsp;&nbsp;&nbsp;&nbsp; H<br>

                  &nbsp;&nbsp;&nbsp;&nbsp; N&nbsp;&nbsp;&nbsp; CA<br>

                  &nbsp;&nbsp;&nbsp; CA&nbsp;&nbsp; HA1<br>

                  &nbsp;&nbsp;&nbsp; CA&nbsp;&nbsp; HA2<br>

                  &nbsp;&nbsp;&nbsp; CA&nbsp;&nbsp;&nbsp; CB<br>

                  &nbsp;&nbsp;&nbsp; CB&nbsp;&nbsp; HB1<br>

                  &nbsp;&nbsp;&nbsp; CB&nbsp;&nbsp; CG1<br>

                  &nbsp;&nbsp;&nbsp; CB&nbsp;&nbsp; CG2<br>

                  &nbsp;&nbsp; CG1&nbsp;&nbsp; CD1<br>

                  &nbsp;&nbsp; CG1&nbsp;&nbsp; CD2<br>

                  &nbsp;&nbsp; CD1&nbsp;&nbsp; HD1<br>

                  &nbsp;&nbsp; CD1&nbsp;&nbsp; CE1<br>

                  &nbsp;&nbsp; CD2&nbsp;&nbsp; HD2<br>

                  &nbsp;&nbsp; CD2&nbsp;&nbsp; CE2<br>

                  &nbsp;&nbsp; CE1&nbsp;&nbsp; HE1<br>

                  &nbsp;&nbsp; CE1&nbsp;&nbsp;&nbsp; CZ<br>

                  &nbsp;&nbsp; CE2&nbsp;&nbsp; HE2<br>

                  &nbsp;&nbsp; CE2&nbsp;&nbsp;&nbsp; CZ<br>

                  &nbsp;&nbsp;&nbsp; CZ&nbsp;&nbsp;&nbsp; Cl<br>

                  &nbsp;&nbsp; CG2&nbsp;&nbsp; HG1<br>

                  &nbsp;&nbsp; CG2&nbsp;&nbsp; HG2<br>

                  &nbsp;&nbsp; CG2&nbsp;&nbsp;&nbsp;&nbsp; C<br>

                  &nbsp;&nbsp;&nbsp;&nbsp; C&nbsp;&nbsp;&nbsp;&nbsp; O<br>

                  &nbsp;&nbsp;&nbsp; -C&nbsp;&nbsp;&nbsp;&nbsp; N<br>

                  <br>

                  and still i got that error!<br>

                  <br>

                  <span style="background-color: rgb(102, 255, 153);">Fatal

                    error:</span><br style="background-color: rgb(102,

                    255, 153);">

                  <span style="background-color: rgb(102, 255, 153);">Atom

                    HB11 not found in rtp database in residue BOC, it

                    looks a bit like HB1</span><br>

                </blockquote>

                <br>

              </div>

            </div>

            a) This structure is phenylalanine with *two* backbone

            methylene spacers, not the one you said in a previous email<br>

            b) Your charge groups are wrong (e.g. number 2)<br>

            c) Your charges are doubtful (CG1 is negative???)<br>

            d) Your atom types are worth checking (should the two

            backbone methylene carbons have those types?)<br>

            e) The atom ordering of the coordinate file and .rtp file

            need to match<br>

            f) The atom coordinates do not correspond to the atom labels

            they are given - presumably you got another bunch of "long

            bond" warnings that you didn't include in your last email.<br>

            <font color="#888888"> <br>

              Mark</font>

            <div>

              <div class="h5"><br>

                <br>

                <blockquote type="cite"><br>

                  <div class="gmail_quote">On Tue, Nov 9, 2010 at 1:12

                    PM, Mark Abraham <span dir="ltr">&lt;<a

                        moz-do-not-send="true"

                        href="mailto:Mark.Abraham@anu.edu.au"

                        target="_blank">Mark.Abraham@anu.edu.au</a>&gt;</span>

                    wrote:<br>

                    <blockquote class="gmail_quote" style="margin: 0pt

                      0pt 0pt 0.8ex; border-left: 1px solid rgb(204,

                      204, 204); padding-left: 1ex;">

                      <div text="#000000" bgcolor="#ffffff">

                        <div> On 9/11/2010 8:19 PM, hengame fallah

                          wrote:

                          <blockquote type="cite">Thanks Justin,<br>

                            actually the protein that i want to simulate

                            consists of two amino acids: PHE and BOC<br>

                            BOC is an unusual amino acid as you know.<br>

                            It has a Cl instead of HZ in PHE and has one

                            extra CH2 in comparison to PHE<br>

                          </blockquote>

                          <br>

                        </div>

                        So that probably means you'll have to pay care

                        to the [bonds] section in the .rtp file. The

                        only bonds GROMACS knows about are the ones in

                        the .rtp. They have to be right. The errors

                        below look like you haven't done it right.

                        <div>

                          <div><br>

                            <br>

                            <blockquote type="cite"> I finally defined a

                              residue BOC in opls .rtp file:<br>

                              &nbsp;<br>

                              [ BOC ]<br>

                              &nbsp;[ atoms ]<br>

                              &nbsp;&nbsp;&nbsp;&nbsp; N&nbsp;&nbsp;&nbsp; opls_238&nbsp;&nbsp; -0.500&nbsp;&nbsp;&nbsp;&nbsp; 1 <br>

                              &nbsp;&nbsp;&nbsp;&nbsp; H&nbsp;&nbsp;&nbsp; opls_241&nbsp;&nbsp;&nbsp; 0.300&nbsp;&nbsp;&nbsp;&nbsp; 1<br>

                              &nbsp;&nbsp;&nbsp; CA&nbsp;&nbsp;&nbsp; opls_224B&nbsp; -0.005&nbsp;&nbsp;&nbsp;&nbsp; 1<br>

                              &nbsp;&nbsp; HA1&nbsp;&nbsp;&nbsp; opls_140&nbsp;&nbsp;&nbsp; 0.060&nbsp;&nbsp;&nbsp;&nbsp; 1<br>

                              &nbsp;&nbsp; HA2&nbsp;&nbsp;&nbsp; opls_140&nbsp;&nbsp;&nbsp; 0.060&nbsp;&nbsp;&nbsp;&nbsp; 1<br>

                              &nbsp;&nbsp;&nbsp; CB&nbsp;&nbsp;&nbsp; opls_149&nbsp;&nbsp;&nbsp; 0.140&nbsp;&nbsp;&nbsp;&nbsp; 2<br>

                              &nbsp;&nbsp; HB1&nbsp;&nbsp;&nbsp; opls_140&nbsp;&nbsp;&nbsp; 0.060&nbsp;&nbsp;&nbsp;&nbsp; 2<br>

                              &nbsp;&nbsp; CG1&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 2<br>

                              &nbsp;&nbsp; CD1&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 3<br>

                              &nbsp;&nbsp; HD1&nbsp;&nbsp;&nbsp; opls_146&nbsp;&nbsp;&nbsp; 0.115&nbsp;&nbsp;&nbsp;&nbsp; 3<br>

                              &nbsp;&nbsp; CD2&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 4<br>

                              &nbsp;&nbsp; HD2&nbsp;&nbsp;&nbsp; opls_146&nbsp;&nbsp;&nbsp; 0.115&nbsp;&nbsp;&nbsp;&nbsp; 4<br>

                              &nbsp;&nbsp; CE1&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 5<br>

                              &nbsp;&nbsp; HE1&nbsp;&nbsp;&nbsp; opls_146&nbsp;&nbsp;&nbsp; 0.115&nbsp;&nbsp;&nbsp;&nbsp; 5<br>

                              &nbsp;&nbsp; CE2&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp; -0.115&nbsp;&nbsp;&nbsp;&nbsp; 6<br>

                              &nbsp;&nbsp; HE2&nbsp;&nbsp;&nbsp; opls_146&nbsp;&nbsp;&nbsp; 0.115&nbsp;&nbsp;&nbsp;&nbsp; 6 <br>

                              &nbsp;&nbsp;&nbsp; CZ&nbsp;&nbsp;&nbsp; opls_145&nbsp;&nbsp;&nbsp; 0.885&nbsp;&nbsp;&nbsp;&nbsp; 7<br>

                              &nbsp;&nbsp;&nbsp; Cl&nbsp;&nbsp;&nbsp; opls_264&nbsp;&nbsp; -1.000&nbsp;&nbsp;&nbsp;&nbsp; 7<br>

                              &nbsp;&nbsp; CG2&nbsp;&nbsp;&nbsp; opls_071&nbsp;&nbsp; -0.005&nbsp;&nbsp;&nbsp;&nbsp; 8<br>

                              &nbsp;&nbsp; HG1&nbsp;&nbsp;&nbsp; opls_140&nbsp;&nbsp;&nbsp; 0.060&nbsp;&nbsp;&nbsp;&nbsp; 8<br>

                              &nbsp;&nbsp; HG2&nbsp;&nbsp;&nbsp; opls_140&nbsp;&nbsp;&nbsp; 0.060&nbsp;&nbsp;&nbsp;&nbsp; 8<br>

                              &nbsp;&nbsp;&nbsp;&nbsp; C&nbsp;&nbsp;&nbsp; opls_235&nbsp;&nbsp;&nbsp; 0.700&nbsp;&nbsp;&nbsp;&nbsp; 9<br>

                              &nbsp;&nbsp;&nbsp;&nbsp; O&nbsp;&nbsp;&nbsp; opls_236&nbsp;&nbsp; -0.700&nbsp;&nbsp;&nbsp;&nbsp; 9<br>

                              <br>

                              the ending part of my PDB is:<br>

                              ...<br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 38&nbsp; HE2 PHE&nbsp;&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -6.946&nbsp;&nbsp;

                              8.455&nbsp;&nbsp; 4.409 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 39&nbsp; CZ&nbsp; PHE&nbsp;&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -5.456&nbsp;

                              10.015&nbsp;&nbsp; 4.624 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 40&nbsp; HZ&nbsp; PHE&nbsp;&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -5.887&nbsp;

                              10.646&nbsp;&nbsp; 3.828 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 41&nbsp; N&nbsp;&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -1.862&nbsp;&nbsp;

                              5.210&nbsp;&nbsp; 5.333 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 42&nbsp; H&nbsp;&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -2.325&nbsp;&nbsp;

                              4.344&nbsp;&nbsp; 5.618 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 43&nbsp; CA&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -1.001&nbsp;&nbsp;

                              5.232&nbsp;&nbsp; 4.169 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 44&nbsp; HA1 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.540&nbsp;&nbsp;

                              6.235&nbsp;&nbsp; 4.026 <br>

                            </blockquote>

                            <br>

                          </div>

                        </div>

                        HA2 is missing here, per your .rtp

                        <div>

                          <div><br>

                            <br>

                            <blockquote type="cite">ATOM&nbsp;&nbsp;&nbsp;&nbsp; 45&nbsp; CB&nbsp;

                              BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -1.797&nbsp;&nbsp; 4.794&nbsp;&nbsp; 2.924 <br>

                              <span style="background-color: rgb(255,

                                102, 102);">ATOM&nbsp;&nbsp;&nbsp;&nbsp; 46 HB1&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp;

                                3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -2.244&nbsp;&nbsp; 3.809&nbsp;&nbsp; 3.204 </span><br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 47&nbsp; CG1 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -2.976&nbsp;&nbsp;

                              5.730&nbsp;&nbsp; 2.589 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 48&nbsp; CG2 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.935&nbsp;&nbsp;

                              4.544&nbsp;&nbsp; 1.698 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 49&nbsp; CD1 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -1.231&nbsp;&nbsp;

                              3.466&nbsp;&nbsp; 0.845 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 50&nbsp; HD1 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -2.070&nbsp;&nbsp;

                              2.790&nbsp;&nbsp; 1.081 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 51&nbsp; CD2 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.120&nbsp;&nbsp;

                              5.408&nbsp;&nbsp; 1.353 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 52&nbsp; HD2 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.357&nbsp;&nbsp;

                              6.277&nbsp;&nbsp; 1.986 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 53&nbsp; CE1 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.471&nbsp;&nbsp;

                              3.236&nbsp; -0.312 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 54&nbsp; HE1 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.717&nbsp;&nbsp;

                              2.381&nbsp; -0.964 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 55&nbsp; CE2 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.881&nbsp;&nbsp;

                              5.182&nbsp;&nbsp; 0.197 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 56&nbsp; HE2 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.706&nbsp;&nbsp;

                              5.870&nbsp; -0.054 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 57&nbsp; CZ&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.591&nbsp;&nbsp;

                              4.093&nbsp; -0.639 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 58&nbsp; C&nbsp;&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -2.565&nbsp;&nbsp;

                              7.148&nbsp;&nbsp; 2.291 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 59&nbsp; O&nbsp;&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -2.716&nbsp;&nbsp;

                              8.035&nbsp;&nbsp; 3.131 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 60&nbsp; CL&nbsp; BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.525&nbsp;&nbsp;

                              3.816&nbsp; -2.062 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 61&nbsp; HA2 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -0.172&nbsp;&nbsp;

                              4.511&nbsp;&nbsp; 4.360 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 62&nbsp; HG1 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -3.530&nbsp;&nbsp;

                              5.331&nbsp;&nbsp; 1.707 <br>

                              ATOM&nbsp;&nbsp;&nbsp;&nbsp; 63&nbsp; HG2 BOC&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -3.708&nbsp;&nbsp;

                              5.729&nbsp;&nbsp; 3.431<br>

                              <br>

                              Now i got t this error:<br>

                              ...<br>

                              There are 1 chains and 0 blocks of water

                              and 3 residues with 63 atoms<br>

                              <br>

                              &nbsp; chain&nbsp; #res #atoms<br>

                              &nbsp; 1 ' '&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp; 63&nbsp; <br>

                              <br>

                              All occupancy fields zero. This is

                              probably not an X-Ray structure<br>

                              Opening library file

                              /usr/share/gromacs/top/ffoplsaa.atp<br>

                              Atomtype 1<br>

                              Reading residue database... (ffoplsaa)<br>

                              Opening library file

                              /usr/share/gromacs/top/ffoplsaa.rtp<br>

                              Residue 57<br>

                              Sorting it all out...<br>

                              Opening library file

                              /usr/share/gromacs/top/ffoplsaa.hdb<br>

                              Opening library file

                              /usr/share/gromacs/top/ffoplsaa-n.tdb<br>

                              Opening library file

                              /usr/share/gromacs/top/ffoplsaa-c.tdb<br>

                              <br>

                              Back Off! I just backed up topol.top to

                              ./#topol.top.69#<br>

                              Processing chain 1 (63 atoms, 3 residues)<br>

                              There are 3 donors and 3 acceptors<br>

                              There are 4 hydrogen bonds<br>

                              Checking for duplicate atoms....<br>

                              Opening library file

                              /usr/share/gromacs/top/specbond.dat<br>

                              7 out of 7 lines of specbond.dat converted

                              succesfully<br>

                              N-terminus: NH3+<br>

                              C-terminus: COO-<br>

                              Now there are 3 residues with 68 atoms<br>

                              Making bonds...<br>

                              Warning: Long Bond (52-53 = 0.334847 nm)<br>

                              Warning: Long Bond (52-55 = 0.334912 nm)<br>

                              Warning: Long Bond (63-64 = 0.271173 nm)<br>

                              Warning: Long Bond (63-65 = 0.347808 nm)<br>

                              Warning: Long Bond (63-66 = 0.31288 nm)<br>

                            </blockquote>

                            <br>

                          </div>

                        </div>

                        This is telling you the connectivity in your

                        .rtp doesn't match the spatial arrangement very

                        well. Go back and check the .rtp file.

                        <div><br>

                          <br>

                          <blockquote type="cite">Opening library file

                            /usr/share/gromacs/top/aminoacids.dat<br>

                            <br>

-------------------------------------------------------<br>

                            Program pdb2gmx, VERSION 4.0.7<br>

                            Source code file:

                            ../../../../src/kernel/add_par.c, line: 233<br>

                            <br>

                            <span style="background-color: rgb(255, 255,

                              0);">Fatal error:</span><br>

                            Atom <span style="background-color:

                              rgb(255, 102, 102);">HB11</span> not found

                            in rtp database in residue BOC, it looks a

                            bit like HB1<br>

                          </blockquote>

                          <br>

                        </div>

                        pdb2gmx is probably hopelessly confused by now.

                        Fix the other issues and try again.<br>

                        <font color="#888888"> <br>

                          Mark</font>

                        <div>

                          <div><br>

                            <br>

                            <blockquote type="cite">

                              -------------------------------------------------------<br>

                              ...<br>

                              <br>

                              What should i do?<br>

                              <br>

                              <br>

                            </blockquote>

                          </div>

                        </div>

                      </div>

                    </blockquote>

                  </div>

                </blockquote>

                <br>

              </div>

            </div>

          </div>

          <br>

          --<br>

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        </blockquote>

      </div>

      <br>

    </blockquote>

    <br>

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