[gmx-users] simulating two peptides in a box
Justin A. Lemkul
jalemkul at vt.edu
Mon Jul 7 20:58:21 CEST 2008
kartik mehra wrote:
>
> Dear Justin,
>
> 1. They are the same protein ( 2 copies of the same protein)
>
OK, that makes life a little easier :-)
> 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 ?
That's the problem. Everything that's in the .top file must be in the
.gro file. Therefore, if you have 4 copies of your protein, you *must*
provide the coordinates for four copies of the protein in the .gro
file. Otherwise, how does mdrun know where they are to do any
calculations?
>
> 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 ... )
>
When you run genbox, use the -p flag, giving the name of your topology
file. It will modify the [ molecules ] section to add the number of
water molecules it placed in your system. Otherwise, genbox prints out
how many water molecules it added, and you can type them in yourself.
Not terribly laborious, either way, really.
-Justin
>
>
>
>
> Thanks
>
>
>
>
> -
> From: *Justin A. Lemkul* <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 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 <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
>
>
>
>
> 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> <mailto: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>
> <mailto: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> <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 <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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