[gmx-users] Unified topology
mark.j.abraham at gmail.com
Thu Oct 15 19:02:39 CEST 2015
No, that's not possible. gmx compare on two .tpr files is useful though.
On Thu, 15 Oct 2015 19:00 Nicolas Cheron <nicolas.cheron.boulot at gmail.com>
> 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.
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