Thankyou. I was able to get .gro file. How can I specify a octahedron box for solvation. I am unable to get the syntax of the command right with -box and -bt.<br>Jaya<br><br><div class="gmail_quote">On Fri, Sep 11, 2009 at 10:52 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
jayalakshmi sridhar wrote:<br>
<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>
I have a homology model of a protein. Te N-terminal is an ASP residue. When I run the command<br>
pdb2gmx -f protein.pdb -o protein.gro -ff G43a1 -p protein.top -i posre.itp<br>
I get the following error-<br>
Atom HA in residue ASP 1 not found in rtp entry with 9 atoms<br>
while sorting atoms. Maybe different protonation state.<br>
Remove this hydrogen or choose a different protonation state.<br>
Option -ignh will ignore all hydrogens in the input.<br>
The protein looks alright in Sybyl. How to get this working? Thanks for the help.<br>
</blockquote>
<br></div></div>
G43a1 is a united-atom force field. Alpha-carbons are not explicitly represented. So if you pass this structure to pdb2gmx, the program assumes you have only the necessary atoms present. If you have unnecessary hydrogens, use -ignh.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Jaya<br>
<br>
<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<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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