<br>Thanks for reply ,The problem is solved .The problem was with topology file .<br><br><div class="gmail_quote">On Fri, Jun 4, 2010 at 4:44 PM, 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>
jani vinod wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
I build a system solvated in water .<br>
Then replicated the system using genconf. Now when I am running grompp i am<br>
getting following warning<br>
Warning: atom name 404 in PH7.top and replicate_systemB.gro does not match (N - C1)<br>
Warning: atom name 405 in PH7.top and replicate_systemB.gro does not match (H1 - C2)<br>
Warning: atom name 406 in PH7.top and replicate_systemB.gro does not match (H2 - C3)<br>
Warning: atom name 407 in PH7.top and replicate_systemB.gro does not match (H3 - N4)<br>
Warning: atom name 408 in PH7.top and replicate_systemB.gro does not match (CA - C5)<br>
Warning: atom name 409 in PH7.top and replicate_systemB.gro does not match (CB - C6)<br>
Warning: atom name 410 in PH7.top and replicate_systemB.gro does not match (CG - O7)<br>
Warning: atom name 411 in PH7.top and replicate_systemB.gro does not match (OD1 - P8)<br>
Warning: atom name 412 in PH7.top and replicate_systemB.gro does not match (OD2 - O9)<br>
Warning: atom name 413 in PH7.top and replicate_systemB.gro does not match (C - O10)<br>
Warning: atom name 414 in PH7.top and replicate_systemB.gro does not match (O - O11)<br>
Warning: atom name 415 in PH7.top and replicate_systemB.gro does not match (N - C12)<br>
Warning: atom name 416 in PH7.top and replicate_systemB.gro does not match (H - C13)<br>
Warning: atom name 417 in PH7.top and replicate_systemB.gro does not match (CA - O14)<br>
Warning: atom name 418 in PH7.top and replicate_systemB.gro does not match (CB - C15)<br>
Warning: atom name 419 in PH7.top and replicate_systemB.gro does not match (C - O16)<br>
Warning: atom name 420 in PH7.top and replicate_systemB.gro does not match (O - C17)<br>
Warning: atom name 421 in PH7.top and replicate_systemB.gro does not match (N - C18)<br>
Warning: atom name 422 in PH7.top and replicate_systemB.gro does not match (H - C19)<br>
Warning: atom name 423 in PH7.top and replicate_systemB.gro does not match (CA - C20)<br>
<br>
and when after ignoring the warning I try to run system my system get distorted.<br>
<br>
</blockquote>
<br></div></div>
Whenever grompp throws warnings like this, don't ignore them and plow ahead, it's a recipe for disaster. The [molecules] section of your topology is out of order with respect to your coordinate file, so parameters for different species are being applied incorrectly.<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;">
<br>
Thanks<br>
vinod<br>
<br>
</blockquote>
<br>
-- <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>
<br>
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