<br><div class="gmail_quote"><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</blockquote><div><br>1. Please disregard the previous mail which was sent from a different email id ....<br>
<br>2. I have copied the relevant portion here ...( previous mail had a wrong command ...I have copied the actual command here)<br><br>Dear Justin, <br><br> Here is the exact error message : ( Here I have
tried to simulate 4 protein molecules in a box ...basically I am
looking at multiple molecule interactions )<br><br><b>grompp -f em.mdp -c nt17_sol.gro -o nt17_em.tpr -p nt17.top</b><br>
<br><b>checking input for internal consistency...<br>calling /usr/bin/cpp...<br>processing topology...<br>Generated 279 of the 1225 non-bonded parameter combinations<br>Excluding 3 bonded neighbours for Protein 4<br>Excluding 2 bonded neighbours for SOL 8813<br>
NOTE:<br> System has non-zero total charge: 4.000000e+00<br><br>processing coordinates...<br>Warning: atom names in nt17.top and nt17_sol.gro don't match (N - OW)<br>Warning: atom names in nt17.top and nt17_sol.gro don't match (H1 - HW1)<br>
Warning: atom names in nt17.top and nt17_sol.gro don't match (H2 - HW2)<br>Warning: atom names in nt17.top and nt17_sol.gro don't match (H3 - OW)<br>Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)<br>
Warning: atom names in nt17.top and nt17_sol.gro don't match (CB - HW2)<br>Warning: atom names in nt17.top and nt17_sol.gro don't match (CG - OW)<br>Warning: atom names in nt17.top and nt17_sol.gro don't match (SD - HW1)<br>
Warning: atom names in nt17.top and nt17_sol.gro don't match (CE - HW2)<br>Warning: atom names in nt17.top and nt17_sol.gro don't match (C - OW)<br>Warning: atom names in nt17.top and nt17_sol.gro don't match (O - HW1)<br>
Warning: atom names in nt17.top and nt17_sol.gro don't match (N - HW2)<br>Warning: atom names in nt17.top and nt17_sol.gro don't match (H - OW)<br>Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)<br>
Warning: atom names in nt17.top and nt17_sol.gro don't match (CB - HW2)<br>Warning: atom names in nt17.top and nt17_sol.gro don't match (C - OW)<br>Warning: atom names in nt17.top and nt17_sol.gro don't match (O - HW1)<br>
Warning: atom names in nt17.top and nt17_sol.gro don't match (N - HW2)<br>Warning: atom names in nt17.top and nt17_sol.gro don't match (H - OW)<br>Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1)<br>
(more than 20 non-matching atom names)<br>WARNING 1 [file "nt17.top", line 1126]:<br> 534 non-matching atom names<br> atom names from nt17.top will be used<br> atom names from nt17_sol.gro will be ignored<br>
<br>double-checking input for internal consistency...<br>renumbering atomtypes...<br>converting bonded parameters...<br># BONDS: 17626<br># G96BONDS: 716<br># ANGLES: 8813<br># G96ANGLES: 1040<br># PDIHS: 372<br>
# IDIHS: 320<br># LJ14: 1104<br>initialising group options...<br>processing index file...<br>Analysing residue names:<br>Opening library file /usr/local/gromacs/3.3.1/64/gnu/ib/share/gromacs/top/aminoacids.dat<br>
There are: 8813 OTHER residues<br>There are: 68 PROTEIN residues<br>There are: 0 DNA residues<br>Analysing Protein...<br>Analysing Other...<br>Making dummy/rest group for T-Coupling containing 27151 elements<br>
Making dummy/rest group for Acceleration containing 27151 elements<br>Making dummy/rest group for Freeze containing 27151 elements<br>Making dummy/rest group for Energy Mon. containing 27151 elements<br>Making dummy/rest group for VCM containing 27151 elements<br>
Number of degrees of freedom in T-Coupling group rest is 81450.00<br>Making dummy/rest group for User1 containing 27151 elements<br>Making dummy/rest group for User2 containing 27151 elements<br>Making dummy/rest group for XTC containing 27151 elements<br>
Making dummy/rest group for Or. Res. Fit containing 27151 elements<br>Making dummy/rest group for QMMM containing 27151 elements<br>T-Coupling has 1 element(s): rest<br>Energy Mon. has 1 element(s): rest<br>Acceleration has 1 element(s): rest<br>
Freeze has 1 element(s): rest<br>User1 has 1 element(s): rest<br>User2 has 1 element(s): rest<br>VCM has 1 element(s): rest<br>XTC has 1 element(s): rest<br>Or. Res. Fit has 1 element(s): rest<br>
QMMM has 1 element(s): rest<br>Checking consistency between energy and charge groups...<br>Calculating fourier grid dimensions for X Y Z<br>Using a fourier grid of 60x60x60, spacing 0.118 0.118 0.118<br>writing run input file...<br>
<br>Back Off! I just backed up nt17_em.tpr to ./#nt17_em.tpr.4#<br>There was 1 warning</b><br><br>Any
suggestions would be appreciated .. Also I do believe that the order
might be a problem..but isnt an inclusion of the no .of molecules meant
to take care of that ?<br>
<br>Thanks </div><div><br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br><br><div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Justin A. Lemkul</b> <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>Date: Mon, Jul 7, 2008 at 10:50 AM<br>
Subject: Re: [gmx-users] simulating two peptides in a box<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br><br><br>Several questions come to mind, aside from trying to sift through your interpretation of error messages. Hint: always show your exact command, followed by the relevant portion of the screen output; that way we don't have to guess what you've been up to :-)<br>
<br>
1. Do you have two different proteins, or are they the same? If they are different, changing the number of Protein molecules in your topology will not be correct. If they are the same, this is fine.<br>
<br>
2. Does the order of your topology follow the order of the coordinate file? When you get warnings about non-matching atom names, you should be alert that something has gone wrong.<br>
<br>
-Justin<br>
<br>
kartik mehra 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="Wj3C7c"><div><div></div><div>
Dear GMX Users,<br>
<br>
I am trying to set up a simulation box with two proteins. I have perused the archives about the methodology of doing so. I tried the recommended option of changing the number of protein molecules in the topology file to 2. However when I run grompp after editconf and genbox, I get warning that the number of co -ordinates do not match (since I had not updated the number of solvent molecules ...) After updating the number of solvent molecules, when I try running grompp again, it shows a warning that the 23644 atom names do not match in top and gro files and that atom names from top files are being chosen .<br>
<br>
Upon subsequent mdrun, the system explodes after a 1-4 interaction warning.<br>
<br>
I was wondering whether anyone could help me out on this ... I do understand that the topic has been discussed pretty often but would appreciate any help ...<br>
<br>
<br>
Cheers<br>
<br>
Kartik<br>
<br>
PS: I have not yet tried the other suggestion of translation and rotation followed by concatenating the two files<br>
<br>
<br></div></div></div></div>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<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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