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<div>Thanks! that did it. It was the wrong column issue.</div>
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<div>However, I can see now that I am getting a non-integer charge for my first nucleic acid chain using the amber03 forcefield. I did replace the aminoacids.dat with the aminoacids-NA.dat contents from the amber port.
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<div><font face="tahoma" size="2">How do I overcome this ?</font></div>
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<font face="Tahoma" color="#000000" size="2"><b>From:</b> gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] On Behalf Of Oliver Grant [olivercgrant@gmail.com]<br>
<b>Sent:</b> Wednesday, August 24, 2011 9:07 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue<br>
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<div>It's reading it as GLY tho so maybe you have NGLY in the wrong column? Maybe try move it over one to the right?<br>
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Oliver<br>
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<div class="gmail_quote">On 24 August 2011 09:47, Kamesh Narasimhan <span dir="ltr">
<<a href="mailto:g0701207@nus.edu.sg">g0701207@nus.edu.sg</a>></span> wrote:<br>
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<div>The termini were changed to NXXX/CXXX and the aminoacids.dat file has these two names as well. So nothing very evident.</div>
<div><font face="tahoma" size="2"></font> </div>
<div><font face="tahoma" size="2">I can see that there was a thread on precisely this issue --- but how it was resolved is not very evident.</font></div>
<div><font face="tahoma" size="2"></font> </div>
<div><a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg18545.html" target="_blank">http://www.mail-archive.com/gmx-users@gromacs.org/msg18545.html</a></div>
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<div class="im"><b>From:</b> <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>] On Behalf Of Jianguo Li [<a href="mailto:ljggmx@yahoo.com.sg">ljggmx@yahoo.com.sg</a>]<br>
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<b>Sent:</b> Wednesday, August 24, 2011 3:46 PM
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<div class="h5"><br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue<br>
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<div style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman,new york,times,serif">Not sure what is the problem. but if you have changed the name of the first/last residue as NXXX/CXXX, you may try to add these two names (NXXX and CXXX) to aminoacids.dat file
(also change the number in the first line).<br>
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Cheers,<br>
Jianguo<br>
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<b><span style="FONT-WEIGHT: bold">From:</span></b> Kamesh Narasimhan <<a href="mailto:g0701207@nus.edu.sg">g0701207@nus.edu.sg</a>><br>
<b><span style="FONT-WEIGHT: bold">To:</span></b> Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
<b><span style="FONT-WEIGHT: bold">Sent:</span></b> Wednesday, 24 August 2011 15:10:13<br>
<b><span style="FONT-WEIGHT: bold">Subject:</span></b> RE: [gmx-users] error:You might need to add atom H to the hydrogen database of residue<br>
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<div>Thanks Jianguo,</div>
<div><font face="tahoma" size="2"></font> </div>
<div>It doesn't seem to make a difference even if i use -ignh -- I still get the same error.</div>
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<font face="Tahoma" color="#000000" size="2"><b>From:</b> <a href="mailto:gmx-users-bounces@gromacs.org">
gmx-users-bounces@gromacs.org</a> [<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>] On Behalf Of Jianguo Li [<a href="mailto:ljggmx@yahoo.com.sg">ljggmx@yahoo.com.sg</a>]<br>
<b>Sent:</b> Wednesday, August 24, 2011 3:06 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue<br>
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<div>you may need to use -ignh option in pdb2gmx.<br>
Jianguo <br>
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<b><span style="FONT-WEIGHT: bold">From:</span></b> Kamesh Narasimhan <<a href="mailto:g0701207@nus.edu.sg">g0701207@nus.edu.sg</a>><br>
<b><span style="FONT-WEIGHT: bold">To:</span></b> "<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
<b><span style="FONT-WEIGHT: bold">Sent:</span></b> Wednesday, 24 August 2011 14:42:28<br>
<b><span style="FONT-WEIGHT: bold">Subject:</span></b> [gmx-users] error:You might need to add atom H to the hydrogen database of residue
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<div dir="ltr"><font face="Tahoma" color="#000000" size="2">Hi all,</font></div>
<div dir="ltr"><font face="tahoma" size="2"></font> </div>
<div dir="ltr"><font face="tahoma" size="2">I am using Gromacs 4.0.5 with the forcefield amber03 in a red hat linux machine to simulate a protein-DNA complex. Eventhough I manually edited my pdb file to adhere to the amber nomenclature, I get the below error.
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<div dir="ltr"><font face="tahoma" size="2">I have not been able to pinpoint where in the pdb file, ffamber03.rtp, and ffamber03.hdb the error could be -- if it's a nomenclature error. Would be great to receive some pointers on this.</font></div>
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<div dir="ltr">pdb2gmx -f prim_amb.pdb -o prim_amb.gro -water spc -ff amber03</div>
<div dir="ltr"><font face="tahoma" size="2">.</font></div>
<div dir="ltr"><font face="tahoma" size="2">.</font></div>
<div dir="ltr"><font face="tahoma" size="2">.</font></div>
<div dir="ltr"><font face="tahoma" size="2">.</font></div>
<div dir="ltr"><font face="tahoma" size="2">.</font></div>
<div dir="ltr">WARNING: atom H is missing in residue GLY 1 in the pdb file<br>
You might need to add atom H to the hydrogen database of residue GLY<br>
in the file ff???.hdb (see the manual)</div>
<p><font face="tahoma" size="2">---------------------------------</font></p>
<p><font face="tahoma" size="2">Program pdb2gmx, VERSION 4.0.5</font></p>
<p><font face="tahoma" size="2">Source code file: pdb2top.C, line: 704</font></p>
<p><font face="tahoma" size="2"></font> </p>
<p><font face="tahoma" size="2">Fatal error:</font></p>
<p><font face="tahoma" size="2">There were 1 missing atoms in molecule Protein_C, if you want to use this incomplete topology anyhow, use the option-missing.</font></p>
<div dir="ltr"> </div>
<div dir="ltr"><font face="tahoma" size="2">I get the error message complaining about a missing hydrogen in the first residue, no matter what that residue is --- say for instance even if I delete the first GLY residue from my pdb file.</font></div>
<div dir="ltr"><font face="tahoma" size="2"></font> </div>
<div dir="ltr"><font face="tahoma" size="2">krish</font></div>
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