[gmx-users] top/itp file to show parameters explicitly
Alan
alanwilter at gmail.com
Wed May 23 10:42:45 CEST 2012
Thanks Justin, you were right. In the end gmxdump helped to clear some
doubts but I wished it would be less painfully.
Cheers,
Alan
On 22 May 2012 12:36, Justin A. Lemkul <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>> 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>.
>>
>> -Justin
>>
>> --
>> ==============================**__==========
>>
>>
>> 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<http://vt.edu/Pages/Personal/justin>
>> <http://www.bevanlab.biochem.**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
>>
>>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**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
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