[gmx-users] no subject

Prasanth G, Research Scholar prasanthghanta at sssihl.edu.in
Mon Mar 16 07:29:03 CET 2020


Hello Faisal,

Easiest way to do this is by navigating to the MD files tab and download
the "Gromacs 4.5.x-5.x.x 54a7" below this warning - "*Warning!* This
molecule contains non-standard atom types not included in the standard
GROMOS 54A7 forcefield..."

The folder contains the procedure to modify the 54a7 forcefield to include
the non-standard atomtypes.
However the easiest way to just include the whole folder in your working
directory (wd) and when you prepare gro from pdb in the first step, you can
choose the option 1 (you will see that you receive a prompt saying this ff
is from the wd).
Hope it helps.

If you are interested in Ligand- protein interaction studies. I would
suggest you to use Amber or Charmm ff. This is because GROMOS is a united
atom ff and an all atom ff might be better in helping you understand these
interactions. Please go through the last part of this thread -
https://www.researchgate.net/post/How_can_I_use_a_Topology_file_generated_by_an_ATB_server

If you want to use Amber ff. you can use ACPYPE which works in conjunction
with AMBER to prepare files necessary in gromacs compatible format. As
antechamber (part of AMBER) is a semi qm/mm technique the parametrization
happens faster , plus it can be done directly on your system.

All the best



-- 
Regards,
Prasanth.


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