Dear Justin, 1. They are the same protein ( 2 copies of the same protein)
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 ? 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 ... ) Thanks > > - > From: Justin A. Lemkul <[EMAIL PROTECTED]> > Date: Mon, Jul 7, 2008 at 11:30 AM > Subject: Re: [gmx-users] simulating two peptides in a box > To: Discussion list for GROMACS users <[email protected]> > > > > > kartik mehra wrote: > >> >> 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 >> >> > > 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? > > If they are different, you will need to have a mechanism something like: > > #include "Protein_A.itp" > #include "Protein_B.itp" > > #include "spc.itp" > > #include "ions.itp" > > to get the desired behavior. > > 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. > > -Justin > > >> >> ---------- Forwarded message ---------- >> From: *Justin A. Lemkul* <[EMAIL PROTECTED] <mailto:[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] >> <mailto:[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] >> <mailto:[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] >> <mailto:[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 <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[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] >> <mailto:[EMAIL PROTECTED]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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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