[gmx-users] CHARMM force field implementation in Gromacs : retrieval of bonded/non-bonded parameters

Nicolas SAPAY nsapay at ucalgary.ca
Wed Sep 13 03:10:27 CEST 2006


I'm trying to use an implementation of the CHARMM force fields in Gromacs
and I'm still a little bit confused about how Gromacs retrieves the
bonded/non-bonded parameters when the .top file is created.   Concretely,
I have :
1. a ffcharmmnb.itp where I have defined specific 1-4 LJ parameters in the
[pairtypes] section

2. a ffcharmmbon.itp where I have defined bonded parameters

3. a ffcharmm.rtp where I have defined the topology of amimo acids, etc.
Since the [bonds], [angles], [dihedral] sections are optional in the .rtp
file, I haven't defined them.

How all these parameters are taken into account when I generate the .top
file with pdb2gmx? When I look in the .top file, I see an [atoms] section
but no [bonds] or [pairs] etc. and the charmm ff doesn't seem to be
included with an #include command. So, are all my specific 1-4 parameters
really taken into account in this case? In fact, I have tried to add somd
bonds and improper but that generates a chunk of warnings when I use

Sorry for this basic question but I'm still new in Gromacs...


[ Nicolas Sapay Ph.D. ]
University of Calgary, Dept. of Biological Sciences
2500 University Dr. NW, Calgary AB, T2N 1N4, Canada
Tel: (403) 220-6869
Fax: (403) 289-9311

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