[gmx-users] Unified topology

[Mark Abraham]

Hi,

No, that's not possible. gmx compare on two .tpr files is useful though.

Mark

On Thu, 15 Oct 2015 19:00 Nicolas Cheron <nicolas.cheron.boulot at gmail.com>
wrote:

> Dear all,
>
> Someone gave me a topology file for a system which was converted from Amber
> (with the CHARMM27 force field). When I compare (via a single point) with a
> topology coming from pdb2gmx, I find some differences between the energetic
> values. I would like to find the cause.
>
> The topology from pdb2gmx has the following format:
> #include "charmm27.ff/forcefield.itp"
> (...)
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     2     1
>     1     3     1
>
> wheras the one I have been given has the following format:
> [ bonds ]
> ;   ai     aj funct   r             k
>      2      1   1    1.0400e-01    3.3723e+05 ;    HT1 - N
>      3      1   1    1.0400e-01    3.3723e+05 ;    HT2 - N
>
> Is there any option in pdb2gmx or grompp to tell the program to write all
> the parameters in the latter format? This would help me to compare
> parameters one by one. I have tried the -pp option of grompp but it "only"
> gathers everything and I still have the same format. If not possible, do
> you have any suggestions?
>
> Thank you for your help or any hints.
>
> Nicolas
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