[gmx-users] Generation of 1-4 nonbonded parameters for CHARMMff

Jong Wha Lee jongwha12 at postech.ac.kr
Fri Jan 11 05:08:29 CET 2013

- I apologize for resubmitting the question as my previous mail was not
properly sent.


Dear gromacs users,


I'm trying to build a new topology and a parameter file of a small organic
molecule. My strategy is to use CGENFF(and  <http://paramchem.org/>
paramchem.org) to generate CHARMM topology and parameter, and then convert
the topology with charmm2gromacs program. I have some questions on the


1) How is the 1-4 parameters generated from the CGENFF file(or more
generally, from charmm ff?)? I was not able to find the parameters
corresponding to the 1-4 nonbonded parameters in original CHARMM parameter

 I'd like to modify some parts of the topology and parameter obtained from
<http://paramchem.org/> paramchem.org(adding new atomtypes, and change
charges etc) before using charmm2gromacs and is curious if this may result
in inconsistency of generated 1-4 parameters. Do I have to also change some
other parameters, such as CMAP, when I'm modifying the charges, bond force
constant, in the sake of correct 1-4 parameters?


2) As I understand from the CHARMM implementation paper of GROMACS, special
features of CHARMM(multiple dihedrals, CMAP, etc) has been taken into the
GROMACS package. I wonder at which step this is done. I guess maybe pdb2gmx
does when it generates .top file, and this is taken into account when grompp
processes .top file. I'm not sure if I'm correct.



Thanks all in advance. I'm really appreciating the various features possible



Jong Wha

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