it is possible that residue 38 is not complete in your structure, in
particular it has no C atom in its backbone, so the tompology cannot be
written for that atom, have you checked if the .top file is complete? <br>
the simplest thing you can try to obtain the correspondent .gro file from a .pdb file is using editconf<br>
<br>
editconf -f input.pdb -o output.gro<br>
<br>
but I suspect thet, il the structure is not complete editconf will stop anyway.<br>
good luck!<br>
<br>
Magiofer<br>
<br>
<br><br><div><span class="gmail_quote">On 9/28/05, <b class="gmail_sendername">Fernando Mattio</b> <<a href="mailto:mattiofer@gmail.com">mattiofer@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Gromacs users,<br>
<br>
I started from a file <span style="font-weight: bold;">1WFA.pdb</span>, and after using the command <br>
<span style="font-weight: bold;">pdb2gmx -f 1WFA.pdb -p WFA.top -o WFA.gro</span><br>
I expected to have the file <span style="font-weight: bold;">WFA.gro</span><br>
However, this fatal error message appears:<span style="font-weight: bold;"> Fatal error: atom C not found in residue 38NH2 while combining tdb and rtp<br>
</span>Probably for this reason the file WFA.gro was not created! But the <span style="font-weight: bold;">WFA.top </span>and the <span style="font-weight: bold;">WFA_A.itp </span>were created!<br>
I really would like to create this .gro file, once I read this kind of
file is better than the .pdb ... I donīt think the command is wrong...
and I started from a pdb file already created! So what is the problem?
How can I correct this? <br>
So please, if anyone knows what should I do to have this .gro file it would be nice.<br>
<br>
Thank you very much in advance,<br><span class="sg">
Fernando.<br>
<span style="font-weight: bold;"></span>
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