[gmx-users] top/itp file to show parameters explicitly

[Alan]

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 <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.
>
> -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
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