<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div style="font-family:times new roman, new york, times, serif;font-size:12pt">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><br>Cheers,<br>Jianguo<br><br><br><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Kamesh Narasimhan <g0701207@nus.edu.sg><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><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></font><br><meta http-equiv="x-dns-prefetch-control" content="off">
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<div>Thanks Jianguo,</div>
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<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 color="#000000" face="Tahoma" size="2"><b>From:</b> gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] On Behalf Of Jianguo Li [ljggmx@yahoo.com.sg]<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 <g0701207@nus.edu.sg><br>
<b><span style="FONT-WEIGHT:bold;">To:</span></b> "gmx-users@gromacs.org" <gmx-users@gromacs.org><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 color="#000000" face="Tahoma" size="2">Hi all,</font></div>
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<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>
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<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>
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<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>
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<div dir="ltr"><font face="tahoma" size="2">krish</font></div>
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