<br>Dear Justin,<br><br>1. They are the same protein ( 2 copies of the same protein)<br><br>2. The order in the .gro file seems fine... Basically it lists the co-ordinates of a single copy of peptide and then the solvent molecule ... I presume since the .top file has 4 copies of the same molecule, this is how the .gro file should look ? <br>
<br>3. Also is there an easier way of dealing with the modification of number of solvent molecules ( since the co-ordinates involve a factor of 3 arising out of the description of SPC atoms ... )<br><br><br><br><br><br>Thanks<br>
<br><div class="gmail_quote"><br><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"><div class="Ih2E3d">-<br>From: <b class="gmail_sendername">Justin A. Lemkul</b> <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
</div><div class="Ih2E3d">Date: Mon, Jul 7, 2008 at 11:30 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></div><div><div></div>
<div class="Wj3C7c"><div><div></div><div><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;">
<br>
Dear Gromacs USers<br>
<br>
<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>
*grompp -f em.mdp -c nt17_sol.gro -o nt17_em.tpr -p nt17.top*<br>
<br>
*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*<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 <br>
<br>
</blockquote>
<br></div></div></div></div>
OK, that's clear now. What's happening is that grompp is finding water molecules where it should be finding protein. Including a "number of protein molecules" does not automatically fix anything, necessarily. Again, I ask, are your proteins the same?<br>
<br>
If they are different, you will need to have a mechanism something like:<br>
<br>
#include "Protein_A.itp"<br>
#include "Protein_B.itp"<br>
<br>
#include "spc.itp"<br>
<br>
#include "ions.itp"<br>
<br>
to get the desired behavior.<br>
<br>
Bottom line - check the order of the molecules in your .gro file, you'll likely find that the order is not the same as the topology expects it.<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;"><div class="Ih2E3d"><div>
<br>
<br>
---------- Forwarded message ----------<br>
From: *Justin A. Lemkul* <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<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></div></div><div><div></div><div class="Wj3C7c"><div><div></div><div>
<mailto:<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<br>
your interpretation of error messages. Hint: always show your<br>
exact command, followed by the relevant portion of the screen<br>
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<br>
they are different, changing the number of Protein molecules in<br>
your topology will not be correct. If they are the same, this is<br>
fine.<br>
<br>
2. Does the order of your topology follow the order of the<br>
coordinate file? When you get warnings about non-matching atom<br>
names, you should be alert that something has gone wrong.<br>
<br>
-Justin<br>
<br>
kartik mehra wrote:<br>
<br>
Dear GMX Users,<br>
<br>
I am trying to set up a simulation box with two proteins. I<br>
have perused the archives about the methodology of doing so. I<br>
tried the recommended option of changing the number of protein<br>
molecules in the topology file to 2. However when I run grompp<br>
after editconf and genbox, I get warning that the number of co<br>
-ordinates do not match (since I had not updated the number of<br>
solvent molecules ...) After updating the number of solvent<br>
molecules, when I try running grompp again, it shows a warning<br>
that the 23644 atom names do not match in top and gro files<br>
and that atom names from top files are being chosen .<br>
<br>
Upon subsequent mdrun, the system explodes after a 1-4<br>
interaction warning.<br>
<br>
I was wondering whether anyone could help me out on this ... I<br>
do understand that the topic has been discussed pretty often<br>
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<br>
and rotation followed by concatenating the two files<br>
<br>
<br>
------------------------------------------------------------------------<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div></div></div></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="Ih2E3d"><div><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="Ih2E3d"><div><br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="Ih2E3d"><div><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>
========================================<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="Ih2E3d"><div><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="Ih2E3d"><div><br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
------------------------------------------------------------------------<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote><div class="Ih2E3d"><div><div></div><div>
<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>
<br>
========================================<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></div></div><br>
</blockquote></div><br>