This is .rtp for [PHE] in opls:<br><br>[ PHE ]<br> [ atoms ]<br>     N    opls_238   -0.500     1<br>     H    opls_241    0.300     1<br>    CA    opls_224B   0.140     1<br>    HA    opls_140    0.060     1<br>    CB    opls_149   -0.005     2<br>
   HB1    opls_140    0.060     2<br>   HB2    opls_140    0.060     2<br>   <span style="background-color: rgb(255, 255, 204);"> CG    opls_145   -0.115     2</span><br>   CD1    opls_145   -0.115     3<br>   HD1    opls_146    0.115     3<br>
   CD2    opls_145   -0.115     4<br>   HD2    opls_146    0.115     4<br>   CE1    opls_145   -0.115     5<br>   HE1    opls_146    0.115     5<br>   CE2    opls_145   -0.115     6<br>   HE2    opls_146    0.115     6 <br>
    CZ    opls_145   -0.115     7 <br>    HZ    opls_146    0.115     7<br>     C    opls_235    0.500     8<br>     O    opls_236   -0.500     8<br> [ bonds ]<br>     N     H<br>     N    CA<br>    CA    HA<br>    CA    CB<br>
    CA     C<br>    CB   HB1<br>    CB   HB2<br>    CB    CG<br>    CG   CD1<br>    CG   CD2<br>   CD1   HD1<br>   CD1   CE1<br>   CD2   HD2<br>   CD2   CE2<br>   CE1   HE1<br>   CE1    CZ<br>   CE2   HE2<br>   CE2    CZ<br>
    CZ    HZ<br>     C     O<br>    -C     N<br><br>and i got the charges by Gaussian.<br>I&#39;m very confused now <img goomoji="361" style="margin: 0pt 0.2ex; vertical-align: middle;" src="cid:361@goomoji.gmail"><br><div class="gmail_quote">
On Tue, Nov 9, 2010 at 2:13 PM, Mark Abraham <span dir="ltr">&lt;<a 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></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     41  N   BOC     3      -1.862   5.210   5.333
      <br>
      ATOM     42  H   BOC     3      -2.325   4.344   5.618
      <br>
      ATOM     43  CA  BOC     3      -1.001   5.232   4.169
      <br>
      ATOM     44  HA1 BOC     3      -0.540   6.235   4.026<br>
      ATOM     45  HA2 BOC     3      -0.172   4.511   4.360
      <br>
      ATOM     46  CB  BOC     3      -1.797   4.794   2.924
      <br>
      ATOM     47  HB1 BOC     3      -2.244   3.809   3.204
      <br>
      ATOM     48  CG1 BOC     3      -2.976   5.730   2.589<br>
      ATOM     49  CD1 BOC     3      -1.231   3.466   0.845
      <br>
      ATOM     50  HD1 BOC     3      -2.070   2.790   1.081
      <br>
      ATOM     51  CD2 BOC     3       0.120   5.408   1.353
      <br>
      ATOM     52  HD2 BOC     3       0.357   6.277   1.986
      <br>
      ATOM     53  CE1 BOC     3      -0.471   3.236  -0.312
      <br>
      ATOM     54  HE1 BOC     3      -0.717   2.381  -0.964
      <br>
      ATOM     55  CE2 BOC     3       0.881   5.182   0.197
      <br>
      ATOM     56  HE2 BOC     3       1.706   5.870  -0.054
      <br>
      ATOM     57  CZ  BOC     3       0.591   4.093  -0.639<br>
      ATOM     58  CG2 BOC     3      -0.935   4.544   1.698<br>
      ATOM     59  HG1 BOC     3      -3.530   5.331   1.707
      <br>
      ATOM     60  HG2 BOC     3      -3.708   5.729   3.431
      <br>
      ATOM     61  C   BOC     3      -2.565   7.148   2.291
      <br>
      ATOM     62  O   BOC     3      -2.716   8.035   3.131
      <br>
      ATOM     63  Cl  BOC     3       1.525   3.816  -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>
       <span style="background-color: rgb(255, 255, 153);">[ atoms ]</span><br>
           N    opls_238   -0.500     1 <br>
           H    opls_241    0.300     1<br>
          CA    opls_224B  -0.005     1<br>
         HA1    opls_140    0.060     1<br>
         HA2    opls_140    0.060     1<br>
          CB    opls_149    0.140     2<br>
         HB1    opls_140    0.060     2<br>
         CG1    opls_145   -0.115     2<br>
         CD1    opls_145   -0.115     3<br>
         HD1    opls_146    0.115     3<br>
         CD2    opls_145   -0.115     4<br>
         HD2    opls_146    0.115     4<br>
         CE1    opls_145   -0.115     5<br>
         HE1    opls_146    0.115     5<br>
         CE2    opls_145   -0.115     6<br>
         HE2    opls_146    0.115     6 <br>
          CZ    opls_145    0.885     7<br>
          Cl    opls_264   -1.000     7<br>
         CG2    opls_071   -0.005     8<br>
         HG1    opls_140    0.060     8<br>
         HG2    opls_140    0.060     8<br>
           C    opls_235    0.700     9<br>
           O    opls_236   -0.700     9<br>
       <span style="background-color: rgb(255, 255, 153);">[ bonds ]</span><br>
           N     H<br>
           N    CA<br>
          CA   HA1<br>
          CA   HA2<br>
          CA    CB<br>
          CB   HB1<br>
          CB   CG1<br>
          CB   CG2<br>
         CG1   CD1<br>
         CG1   CD2<br>
         CD1   HD1<br>
         CD1   CE1<br>
         CD2   HD2<br>
         CD2   CE2<br>
         CE1   HE1<br>
         CE1    CZ<br>
         CE2   HE2<br>
         CE2    CZ<br>
          CZ    Cl<br>
         CG2   HG1<br>
         CG2   HG2<br>
         CG2     C<br>
           C     O<br>
          -C     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 &quot;long bond&quot; warnings
    that you didn&#39;t include in your last email.<br><font color="#888888">
    <br>
    Mark</font><div><div></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 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&#39;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&#39;t done it right.
            <div>
              <div><br>
                <br>
                <blockquote type="cite"> I finally defined a residue BOC
                  in opls .rtp file:<br>
                   <br>
                  [ BOC ]<br>
                   [ atoms ]<br>
                       N    opls_238   -0.500     1 <br>
                       H    opls_241    0.300     1<br>
                      CA    opls_224B  -0.005     1<br>
                     HA1    opls_140    0.060     1<br>
                     HA2    opls_140    0.060     1<br>
                      CB    opls_149    0.140     2<br>
                     HB1    opls_140    0.060     2<br>
                     CG1    opls_145   -0.115     2<br>
                     CD1    opls_145   -0.115     3<br>
                     HD1    opls_146    0.115     3<br>
                     CD2    opls_145   -0.115     4<br>
                     HD2    opls_146    0.115     4<br>
                     CE1    opls_145   -0.115     5<br>
                     HE1    opls_146    0.115     5<br>
                     CE2    opls_145   -0.115     6<br>
                     HE2    opls_146    0.115     6 <br>
                      CZ    opls_145    0.885     7<br>
                      Cl    opls_264   -1.000     7<br>
                     CG2    opls_071   -0.005     8<br>
                     HG1    opls_140    0.060     8<br>
                     HG2    opls_140    0.060     8<br>
                       C    opls_235    0.700     9<br>
                       O    opls_236   -0.700     9<br>
                  <br>
                  the ending part of my PDB is:<br>
                  ...<br>
                  ATOM     38  HE2 PHE     2      -6.946   8.455   4.409
                  <br>
                  ATOM     39  CZ  PHE     2      -5.456  10.015   4.624
                  <br>
                  ATOM     40  HZ  PHE     2      -5.887  10.646   3.828
                  <br>
                  ATOM     41  N   BOC     3      -1.862   5.210   5.333
                  <br>
                  ATOM     42  H   BOC     3      -2.325   4.344   5.618
                  <br>
                  ATOM     43  CA  BOC     3      -1.001   5.232   4.169
                  <br>
                  ATOM     44  HA1 BOC     3      -0.540   6.235   4.026
                  <br>
                </blockquote>
                <br>
              </div>
            </div>
            HA2 is missing here, per your .rtp
            <div>
              <div><br>
                <br>
                <blockquote type="cite">ATOM     45  CB  BOC     3     
                  -1.797   4.794   2.924 <br>
                  <span style="background-color: rgb(255, 102, 102);">ATOM    
                    46 HB1  BOC     3      -2.244   3.809   3.204 </span><br>
                  ATOM     47  CG1 BOC     3      -2.976   5.730   2.589
                  <br>
                  ATOM     48  CG2 BOC     3      -0.935   4.544   1.698
                  <br>
                  ATOM     49  CD1 BOC     3      -1.231   3.466   0.845
                  <br>
                  ATOM     50  HD1 BOC     3      -2.070   2.790   1.081
                  <br>
                  ATOM     51  CD2 BOC     3       0.120   5.408   1.353
                  <br>
                  ATOM     52  HD2 BOC     3       0.357   6.277   1.986
                  <br>
                  ATOM     53  CE1 BOC     3      -0.471   3.236  -0.312
                  <br>
                  ATOM     54  HE1 BOC     3      -0.717   2.381  -0.964
                  <br>
                  ATOM     55  CE2 BOC     3       0.881   5.182   0.197
                  <br>
                  ATOM     56  HE2 BOC     3       1.706   5.870  -0.054
                  <br>
                  ATOM     57  CZ  BOC     3       0.591   4.093  -0.639
                  <br>
                  ATOM     58  C   BOC     3      -2.565   7.148   2.291
                  <br>
                  ATOM     59  O   BOC     3      -2.716   8.035   3.131
                  <br>
                  ATOM     60  CL  BOC     3       1.525   3.816  -2.062
                  <br>
                  ATOM     61  HA2 BOC     3      -0.172   4.511   4.360
                  <br>
                  ATOM     62  HG1 BOC     3      -3.530   5.331   1.707
                  <br>
                  ATOM     63  HG2 BOC     3      -3.708   5.729   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>
                    chain  #res #atoms<br>
                    1 &#39; &#39;     3     63  <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&#39;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>

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