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

[Javier Cerezo]

The actual parameters are listed in the ffbonded.itp file located in the 
folder of the corresponding force field, under [ dihedraltypes ] section.

Javier

El 21/05/12 14:43, Alan escribió:
> 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.
>
> Thanks,
>
> Alan
>
> -- 
> Alan Wilter SOUSA da SILVA, DSc
> Bioinformatician, UniProt - PANDA, EMBL-EBI
> CB10 1SD, Hinxton, Cambridge, UK
> +44 1223 49 4588
>
>
>

-- 
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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