[gmx-users] simulating two peptides in a box
Justin A. Lemkul
jalemkul at vt.edu
Mon Jul 7 20:30:42 CEST 2008
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* <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 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 <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
>
>
> 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
>
>
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> --
> ========================================
>
> 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
>
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--
========================================
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
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