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

[Justin A. Lemkul]

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

-- 
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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

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