[gmx-users] top/itp file to show parameters explicitly
Mark Abraham
Mark.Abraham at anu.edu.au
Wed May 23 10:47:05 CEST 2012
On 23/05/2012 6:42 PM, Alan wrote:
> Thanks Justin, you were right. In the end gmxdump helped to clear some
> doubts but I wished it would be less painfully.
One useful approach is to simplify the system as much as possible before
producing the .tpr and using gmxdump. The necessary cross-referencing is
easier to see when the complexity of the contents is low.
Mark
>
> Cheers,
>
> Alan
>
> On 22 May 2012 12:36, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> On 5/22/12 12:46 PM, Alan wrote:
>
> Hi Justin, your suggestion got close. However, let me give an
> example. You can
> use the Gly-Gly-Gly example I am attaching and do this:
>
> pdb2gmx -ff amber99sb -f aGGG.pdb -o aGGG_.pdb -p aGGG.top
> -water none
> /sw/bin/grompp -c aGGG_.pdb -p aGGG.top -f SPE.mdp -o aGGG.tpr
> -pp aGGGp.top
>
> if you look at aGGGp.top I can't find which parameters were
> used for
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2
> c3 c4 c5
> 2 1 5 6 9
>
> I.e., for proper dihedral (H1- N- CA- HA1), I can't find
> in amber99sb.ff/forcefield.itp any combination that handles
> parameters for
> X-N-CA-X or X-CA-N-X, so how grompp is interpreting this dihedral?
>
>
> Make sure you're looking at types, not names. The type sequence
> here is H-N3-CT-HP, which I think is mapped to this dihedral:
>
> X CT N3 X 9 0.0 0.65084 3 ; JCC,7,(1986),230
>
> Running gmxdump on the .tpr file will show it for sure; I had
> assumed it would be in the post-processed topology as well, but I
> guess not.
>
> -Justin
>
> Thanks,
>
> Alan
>
> On 21 May 2012 18:50, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> On 5/21/12 2:43 PM, Alan wrote:
>
> Hi there,
>
> Is there an option in pdb2gmx that when generating the
> top/itp file, it
> could
> show the parameters explicitly? e.g.:
>
> Instead of:
> [ dihedrals ]
> ; ai aj ak al funct c0
> c1 c2
> c3
> 5 13 11 12 4
> 11 15 13 14 4
> 15 23 21 22 4
> 21 25 23 24 4
> 25 32 31 33 4
>
> (my hard hand modifications)
>
> [ dihedrals ] ; impropers
> ; treated as propers in GROMACS to use correct AMBER
> analytical function
> ; i j k l func phase kd pn
> 5 13 11 12 4 180.00 43.93200
> 2 ; CA- N-
> C- O
> 11 15 13 14 4 180.00 4.60240
> 2 ; C- CA-
> N- H
> 15 23 21 22 4 180.00 43.93200
> 2 ; CA- N-
> C- O
> 21 25 23 24 4 180.00 4.60240
> 2 ; C- CA-
> N- H
> 25 32 31 33 4 180.00 43.93200
> 2 ; CA- OC1-
> C- OC2
>
> I mean, if the parameters that are hiding in e.g.
> ...gromacs/top/amber99sb.ff
> could be showed in the top/itp file for human readers,
> that would be great.
>
>
> You can obtain these parameters (I believe) by running
> grompp with the -pp
> option. If you think it would be a useful feature for
> pdb2gmx, file a
> feature request on redmine.gromacs.org
> <http://redmine.gromacs.org> <http://redmine.gromacs.org>.
>
> -Justin
>
> --
> ==============================__==========
>
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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
> <http://vt.edu/Pages/Personal/justin>
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================__==========
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> --
> Alan Wilter SOUSA da SILVA, DSc
> Bioinformatician, UniProt - PANDA, EMBL-EBI
> CB10 1SD, Hinxton, Cambridge, UK
> +44 1223 49 4588 <tel:%2B44%201223%2049%204588>
>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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> --
> Alan Wilter SOUSA da SILVA, DSc
> Bioinformatician, UniProt - PANDA, EMBL-EBI
> CB10 1SD, Hinxton, Cambridge, UK
> +44 1223 49 4588
>
>
>
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