[gmx-users] Unified topology
nicolas.cheron.boulot at gmail.com
Thu Oct 15 18:59:40 CEST 2015
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:
[ 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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