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    On 20/04/2012 9:02 PM, Sundar Jubilant wrote:
    <blockquote
      cite="mid:8CEECFC44F2F8A7-410-3CDFE@webmail-d047.sysops.aol.com"
      type="cite"><font color="black" face="arial" size="2"><font
          color="black" face="arial" size="2">
          <div> <br>
          </div>
          <div> <font face="Arial, Helvetica, sans-serif">Dear Abraham,<br>
              <br>
              How would it work if I remove the hydrogen atoms that I
              wish to ignore from my input co-ordinate file? The pdb2gmx
              tries to add the missing hydorgen atoms for which the .hdb
              doesn't have information.<br>
            </font></div>
        </font></font></blockquote>
    <br>
    You've never actually told us what hydrogens you want to ignore, so
    you're making it hard to help you.<br>
    <br>
    Mark<br>
    <br>
    <blockquote
      cite="mid:8CEECFC44F2F8A7-410-3CDFE@webmail-d047.sysops.aol.com"
      type="cite"><font color="black" face="arial" size="2"><font
          color="black" face="arial" size="2">
          <div><font face="Arial, Helvetica, sans-serif">
              <br>
              In my case here, I can consider heme as a ligand instead
              of having it as protein since it doesn't need to be the
              part of the protein.<br>
              <br>
              Thanks for your information.<br>
              Sundar<br>
            </font>
          </div>
          <div> <br>
          </div>
          <div
            style="font-family:arial,helvetica;font-size:10pt;color:black">-----Original
            Message-----<br>
            From: Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au">&lt;Mark.Abraham@anu.edu.au&gt;</a><br>
            To: Discussion list for GROMACS users
            <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org">&lt;gmx-users@gromacs.org&gt;</a><br>
            Sent: Fri, Apr 20, 2012 6:42 pm<br>
            Subject: Re: [gmx-users] Heme group with CHARMM27 FF<br>
            <br>
            <div id="AOLMsgPart_2_3edbbaac-164b-4d4b-bb0b-675bb06150c4">
              On 20/04/2012 7:33 PM, Sundar Jubilant wrote:
              <blockquote type="cite"><font color="black" face="arial"
                  size="2"><font color="black" face="arial" size="2">
                    <div> Dear Abraham,<br>
                      <br>
                      I am ignoring hydrogens for the protein residues
                      since I am not sure if the Gromacs has an option
                      to ignore hydrogen only for pretein residues but
                      not for the heme complexed with it.<br>
                    </div>
                  </font></font></blockquote>
              <br>
              No, there is no ability to ignore them selectively - but
              if you want to ignore any of them, you have to address the
              heme hydrogen database issue, or go and remove the
              hydrogen atoms that you wish to ignore from your input
              coordinate file.<br>
              <br>
              <blockquote type="cite"><font color="black" face="arial"
                  size="2"><font color="black" face="arial" size="2">
                    <div> <br>
                      One of my colleagues suggested to treat the Heme
                      as an ligand not as a part of the protein to solve
                      this issue. How would that really affect the
                      accuracy of the simulation?<br>
                    </div>
                  </font></font></blockquote>
              <br>
              It's not a question of accuracy, but rather that if you
              have bonded interactions between heme and protein, they
              have to be part of the same [moleculetype], which is what
              pdb2gmx is struggling to generate.<br>
              <br>
              Mark<br>
              <br>
              <blockquote type="cite"><font color="black" face="arial"
                  size="2"><font color="black" face="arial" size="2">
                    <div> <br>
                      Thanks<br>
                      Sundar<br>
                    </div>
                    <div> <br>
                    </div>
                    <div> <br>
                    </div>
                    <div
                      style="font-family:arial,helvetica;font-size:10pt;color:black">-----Original

                      Message-----<br>
                      From: Mark Abraham <a moz-do-not-send="true"
                        class="moz-txt-link-rfc2396E"
                        href="mailto:Mark.Abraham@anu.edu.au">&lt;Mark.Abraham@anu.edu.au&gt;</a><br>
                      To: Discussion list for GROMACS users <a
                        moz-do-not-send="true"
                        class="moz-txt-link-rfc2396E"
                        href="mailto:gmx-users@gromacs.org">&lt;gmx-users@gromacs.org&gt;</a><br>
                      Sent: Fri, Apr 20, 2012 3:57 pm<br>
                      Subject: Re: [gmx-users] Heme group with CHARMM27
                      FF<br>
                      <br>
                      <div
                        id="AOLMsgPart_2_f2d1812f-0eae-4513-a2a5-23a35a3ae4bd">
                        On 20/04/2012 4:38 PM, Sundar Jubilant wrote:
                        <blockquote type="cite"><font color="black"
                            face="arial" size="2"><font color="black"
                              face="arial" size="2">
                              <div> <br>
                              </div>
                              <div> <font face="Arial, Helvetica,
                                  sans-serif">Dear Abraham,<br>
                                  <br>
                                  Thanks for your email. I have already
                                  read the manual to solve the problem
                                  but I wasn't successful.<br>
                                </font></div>
                            </font></font></blockquote>
                        <br>
                        That's good to say (particularly the first time
                        you post a request for help, else you'll just
                        get told to go and read), but is unlikely to get
                        much help because you haven't identified a
                        specific problem. You'd like the ability to
                        build hydrogen atoms on a heme residue. pdb2gmx
                        has to have a specific recipe for doing that.
                        The manual describes the required format and
                        gives an example. Someone's going to have to do
                        some work.<br>
                        <br>
                        <blockquote type="cite"><font color="black"
                            face="arial" size="2"><font color="black"
                              face="arial" size="2">
                              <div><font face="Arial, Helvetica,
                                  sans-serif"> <br>
                                  I need little more detailed answer to
                                  solve the problem. <br>
                                  <br>
                                  By the way, here is the full command
                                  line for which I got the error.<br>
                                  <br>
                                  $ pdb2gmx -f CYP.pdb -o CYP_CHARMM.pdb
                                  -p CYP1_CHARMM.top -i CYP_CHARMM.itp
                                  -ignh<br>
                                </font></div>
                            </font></font></blockquote>
                        <br>
                        If you don't ignore hydrogens, and they're
                        already correct, you don't need to re-generate
                        them...<br>
                        <br>
                        Mark<br>
                        <br>
                        <blockquote type="cite"><font color="black"
                            face="arial" size="2"><font color="black"
                              face="arial" size="2">
                              <div><font face="Arial, Helvetica,
                                  sans-serif"> <br>
                                  The error is<br>
                                  <br>
                                </font><font color="black" face="arial"
                                  size="2"><font color="black"
                                    face="arial" size="2"><font
                                      color="black" face="arial"
                                      size="2"><font face="Arial,
                                        Helvetica, sans-serif">WARNING:
                                        atom HA is missing in residue
                                        HEM 513 in the pdb file<br>
                                        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; You might need to add
                                        atom HA to the hydrogen database
                                        of building block HEME<br>
                                        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; in the file
                                        aminoacids.hdb (see the manual)<br>
                                        <br>
                                        <br>
                                        WARNING: atom HB is missing in
                                        residue HEM 513 in the pdb file<br>
                                        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; You might need to add
                                        atom HB to the hydrogen database
                                        of building block HEME<br>
                                        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; in the file
                                        aminoacids.hdb (see the manual)<br>
                                        <br>
                                        <br>
                                        WARNING: atom HC is missing in
                                        residue HEM 513 in the pdb file<br>
                                        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; You might need to add
                                        atom HC to the hydrogen database
                                        of building block HEME<br>
                                        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; in the file
                                        aminoacids.hdb (see the manual)<br>
                                        <br>
                                        .<br>
                                        .<br>
                                        .<br>
                                        .<br>
                                        .<br>
-------------------------------------------------------<br>
                                        Program pdb2gmx, VERSION 4.5.3<br>
                                        Source code file: pdb2top.c,
                                        line: 1449<br>
                                        <br>
                                        Fatal error:<br>
                                        There were 30 missing atoms in
                                        molecule Protein, if you want to
                                        use this incomplete topology
                                        anyhow, use the option -missing<br>
                                        For more information and tips
                                        for troubleshooting, please
                                        check the GROMACS<br>
                                        website at <a
                                          moz-do-not-send="true"
                                          class="moz-txt-link-freetext"
                                          target="_blank"
                                          href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
                                        <br>
                                        Thanks.<br>
                                        <br>
                                        Sundar Jubilant<br>
                                      </font></font></font></font><font
                                  face="Arial, Helvetica, sans-serif"><br>
                                </font> </div>
                              <div> <br>
                              </div>
                              <div
                                style="font-family:arial,helvetica;font-size:10pt;color:black">-----Original


                                Message-----<br>
                                From: Mark Abraham <a
                                  moz-do-not-send="true"
                                  class="moz-txt-link-rfc2396E"
                                  href="mailto:Mark.Abraham@anu.edu.au">&lt;Mark.Abraham@anu.edu.au&gt;</a><br>
                                To: Discussion list for GROMACS users <a
                                  moz-do-not-send="true"
                                  class="moz-txt-link-rfc2396E"
                                  href="mailto:gmx-users@gromacs.org">&lt;gmx-users@gromacs.org&gt;</a><br>
                                Sent: Fri, Apr 20, 2012 2:17 pm<br>
                                Subject: Re: [gmx-users] Heme group with
                                CHARMM27 FF<br>
                                <br>
                                <div
                                  id="AOLMsgPart_2_989141e2-b2c9-4465-ab1e-9f4619eb8577">
                                  On 20/04/2012 2:33 PM, Sundar Jubilant
                                  wrote:
                                  <blockquote type="cite"><font
                                      color="black" face="arial"
                                      size="2"><font color="black"
                                        face="arial" size="2"><font
                                          face="Arial, Helvetica,
                                          sans-serif">Dear gmx-users,<br>
                                          <br>
                                          I am new to Gromacs and trying
                                          to simulate a protein with a
                                          heme group using CHARMM27 ff
                                          in Gromacs 4.5.3. I have
                                          received the following error
                                          while running pdb2gmx .<br>
                                        </font></font></font></blockquote>
                                  <br>
                                  When asking for help, please give your
                                  full command lines and/or interactive
                                  selections so that we can know more
                                  context.<br>
                                  <br>
                                  <blockquote type="cite"><font
                                      color="black" face="arial"
                                      size="2"><font color="black"
                                        face="arial" size="2"><font
                                          face="Arial, Helvetica,
                                          sans-serif"> <br>
                                          WARNING: atom HA is missing in
                                          residue HEM 513 in the pdb
                                          file<br>
                                          &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; You might need to add
                                          atom HA to the hydrogen
                                          database of building block
                                          HEME<br>
                                          &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; in the file
                                          aminoacids.hdb (see the
                                          manual)<br>
                                          <br>
                                          <br>
                                          WARNING: atom HB is missing in
                                          residue HEM 513 in the pdb
                                          file<br>
                                          &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; You might need to add
                                          atom HB to the hydrogen
                                          database of building block
                                          HEME<br>
                                          &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; in the file
                                          aminoacids.hdb (see the
                                          manual)<br>
                                          <br>
                                          <br>
                                          WARNING: atom HC is missing in
                                          residue HEM 513 in the pdb
                                          file<br>
                                          &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; You might need to add
                                          atom HC to the hydrogen
                                          database of building block
                                          HEME<br>
                                          &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; in the file
                                          aminoacids.hdb (see the
                                          manual)<br>
                                          <br>
                                          .<br>
                                          .<br>
                                          .<br>
                                          .<br>
                                          .<br>
-------------------------------------------------------<br>
                                          Program pdb2gmx, VERSION 4.5.3<br>
                                          Source code file: pdb2top.c,
                                          line: 1449<br>
                                          <br>
                                          Fatal error:<br>
                                          There were 30 missing atoms in
                                          molecule Protein, if you want
                                          to use this incomplete
                                          topology anyhow, use the
                                          option -missing<br>
                                          For more information and tips
                                          for troubleshooting, please
                                          check the GROMACS<br>
                                          website at <a
                                            moz-do-not-send="true"
                                            class="moz-txt-link-freetext"
                                            target="_blank"
                                            href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
                                          <br>
                                          Can anyone help how can I
                                          generate and add hydrogen
                                          database information for heme
                                          to be used with CHARMM27 ff?</font></font></font><br>
                                  </blockquote>
                                  <font color="black"><font size="2"><font
                                        face="Arial, Helvetica,
                                        sans-serif"><br>
                                        You'll have to read the
                                        applicable sections of manual
                                        chapter 5, make a local copy of
                                        the charmm27.ff folder in your
                                        working directory and editing
                                        aminoacids.hdb to add the
                                        generation information. When
                                        you're done, please post your
                                        efforts so that others might be
                                        able to benefit from them in
                                        future. (Also, search first in
                                        case this has already happened!)<br>
                                        <br>
                                        Mark<br>
                                      </font></font></font> </div>
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                                  id="AOLMsgPart_3_989141e2-b2c9-4465-ab1e-9f4619eb8577"
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                                  Tahoma, Verdana, Arial,
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                                  <pre style="font-size: 9pt;"><tt>-- 
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</tt></pre>
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                        <pre style="font-size: 9pt;"><tt>-- 
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<a moz-do-not-send="true" target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>
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              <pre style="font-size: 9pt;"><tt>-- 
gmx-users mailing list    <a moz-do-not-send="true" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
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before posting!
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