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

[Justin A. Lemkul]

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://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
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>

-- 
========================================

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

========================================