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?
Thanks,
Alan
On 21 May 2012 18:50, Justin A. Lemkul <[email protected]> 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.
>
> -Justin
>
> --
> ==============================**==========
>
> 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
aGGG.pdb
Description: Protein Databank data
SPE.mdp
Description: Binary data
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