Thank you so much Justin, that really helped :)<br><br><div class="gmail_quote">On Mon, Apr 25, 2011 at 12:17 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
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prerna bhardwaj wrote:<br>
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Dear Gromacs User,<br>
<br>
I want to simulate my protein at a specific pH. Using H++ server I have generated my .pdb file at pH 5. But pdb2gmx is showing all the usual fatal error "like "Atom HB3 in residue MET 1 not found in rtp entry with 17 atoms". But I can't use -ignh option, because it is bringing back at the same normal stage. So what should I do I want to carry out simulation at pH 5.<br>
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It sounds like you should indeed be using -ignh because you have a malformed input. Under no conditions should the beta-carbon of methionine ever have three protons. Carbon atoms can't have five bonds. Either the atom naming in your .pdb file is wrong (which will cause pdb2gmx to fail) or the protonation state is wrong (which will cause pdb2gmx to fail in the absence of -ignh).<br>
<br>
You can set the protonation state of any titratable residues and termini using pdb2gmx -inter, in concert with -ignh, which appears to be necessary in your case.<br>
<br>
-Justin<br>
<br>
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Thanks<br>
Prerna<br>
<br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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