[gmx-users] simulating two peptides in a box
kartik mehra
hrahesh at gmail.com
Mon Jul 7 20:42:27 CEST 2008
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 <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>
>
>
>
>
> 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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>>
>> ------------------------------------------------------------------------
>>
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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
>
> ========================================
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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