[AMBER] Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME

From: Matthew Fisher <matthew.fisher.stcatz.ox.ac.uk>
Date: Tue, 23 Oct 2018 21:10:32 +0000

Hi all,

I have a slightly unusual situation. I've found HEME parameters for a ferryl intermediate species, written for AMBER (https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21922) that I wish to use with the AMBER99sb-ILDN ff in GROMACS. However, in doing so, I've hit a stumbling block. GAFF parameters are used for the impropers and dihedrals and I'm struggling to find the necessary ones to add to the ffbonded.itp file in GROMACS.

An old tutorial online gives this advice, although when I tried to do this it recorded a failure.

"First add all the dihedrals specified in the frcmod. Then use Ambertools to generate a coordinate and topology file with the loaded mol2 and frcmod files but don't load the GAFF parameters. Ambertools will tell you which impropers and dihedrals you have to add from the GAFF.dat because it could not find them in the frcmod."

Any advice would be appreciated.

Many thanks,

Matthew Fisher

Matthew Fisher
DPhil Candidate in Inorganic Chemistry (L.L.Wong Group)
AMBER mailing list
Received on Tue Oct 23 2018 - 14:30:01 PDT
Custom Search