> Dear Gromacs USers
1. Please disregard the previous mail which was sent from a different email id .... 2. I have copied the relevant portion here ...( previous mail had a wrong command ...I have copied the actual command here) Dear Justin, 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 ) *grompp -f em.mdp -c nt17_sol.gro -o nt17_em.tpr -p nt17.top* *checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 4 Excluding 2 bonded neighbours for SOL 8813 NOTE: System has non-zero total charge: 4.000000e+00 processing coordinates... Warning: atom names in nt17.top and nt17_sol.gro don't match (N - OW) Warning: atom names in nt17.top and nt17_sol.gro don't match (H1 - HW1) Warning: atom names in nt17.top and nt17_sol.gro don't match (H2 - HW2) Warning: atom names in nt17.top and nt17_sol.gro don't match (H3 - OW) Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1) Warning: atom names in nt17.top and nt17_sol.gro don't match (CB - HW2) Warning: atom names in nt17.top and nt17_sol.gro don't match (CG - OW) Warning: atom names in nt17.top and nt17_sol.gro don't match (SD - HW1) Warning: atom names in nt17.top and nt17_sol.gro don't match (CE - HW2) Warning: atom names in nt17.top and nt17_sol.gro don't match (C - OW) Warning: atom names in nt17.top and nt17_sol.gro don't match (O - HW1) Warning: atom names in nt17.top and nt17_sol.gro don't match (N - HW2) Warning: atom names in nt17.top and nt17_sol.gro don't match (H - OW) Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1) Warning: atom names in nt17.top and nt17_sol.gro don't match (CB - HW2) Warning: atom names in nt17.top and nt17_sol.gro don't match (C - OW) Warning: atom names in nt17.top and nt17_sol.gro don't match (O - HW1) Warning: atom names in nt17.top and nt17_sol.gro don't match (N - HW2) Warning: atom names in nt17.top and nt17_sol.gro don't match (H - OW) Warning: atom names in nt17.top and nt17_sol.gro don't match (CA - HW1) (more than 20 non-matching atom names) WARNING 1 [file "nt17.top", line 1126]: 534 non-matching atom names atom names from nt17.top will be used atom names from nt17_sol.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 17626 # G96BONDS: 716 # ANGLES: 8813 # G96ANGLES: 1040 # PDIHS: 372 # IDIHS: 320 # LJ14: 1104 initialising group options... processing index file... Analysing residue names: Opening library file /usr/local/gromacs/3.3.1/64/gnu/ib/share/gromacs/top/aminoacids.dat There are: 8813 OTHER residues There are: 68 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... Making dummy/rest group for T-Coupling containing 27151 elements Making dummy/rest group for Acceleration containing 27151 elements Making dummy/rest group for Freeze containing 27151 elements Making dummy/rest group for Energy Mon. containing 27151 elements Making dummy/rest group for VCM containing 27151 elements Number of degrees of freedom in T-Coupling group rest is 81450.00 Making dummy/rest group for User1 containing 27151 elements Making dummy/rest group for User2 containing 27151 elements Making dummy/rest group for XTC containing 27151 elements Making dummy/rest group for Or. Res. Fit containing 27151 elements Making dummy/rest group for QMMM containing 27151 elements T-Coupling has 1 element(s): rest Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 60x60x60, spacing 0.118 0.118 0.118 writing run input file... Back Off! I just backed up nt17_em.tpr to ./#nt17_em.tpr.4# There was 1 warning* 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 ? Thanks > > > ---------- Forwarded message ---------- > From: Justin A. Lemkul <[EMAIL PROTECTED]> > Date: Mon, Jul 7, 2008 at 10:50 AM > Subject: Re: [gmx-users] simulating two peptides in a box > To: Discussion list for GROMACS users <[email protected]> > > > 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 :-) > > 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. > > 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. > > -Justin > > kartik mehra wrote: > >> Dear GMX Users, >> >> 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 . >> >> Upon subsequent mdrun, the system explodes after a 1-4 interaction >> warning. >> >> 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 ... >> >> >> Cheers >> >> Kartik >> >> PS: I have not yet tried the other suggestion of translation and rotation >> followed by concatenating the two files >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >
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