[gmx-users] Unified topology

Nicolas Cheron nicolas.cheron.boulot at gmail.com
Thu Oct 15 18:59:40 CEST 2015

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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