Ooops, forgot
The acpype tool can be found here: https://github.com/alanwilter/acpype
HTH
Stéphane
________________________________________
De : ABEL Stephane
Envoyé : mercredi 24 octobre 2018 10:45
À : AMBER Mailing List
Objet : RE:[AMBER] Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME
Hello,
It is not a real if you have all the AMBER parameters for HEME in a given oxydation state.
1) Build the AMBER (non)bonded parameters in the AMBER format (see for instance this site
http://research.bmh.manchester.ac.uk/bryce/amber/) and the data given in the Cheatham paper . In this site you will also find the prep and FRCMOD files for heme
2) use ACEPYPE (
https://pypi.org/project/acpype/) to convert the AMBER parameters into the GROMACS format and obtain the topol.top, ffbonded.itp and ffnonbonded.itp.
The step 2) can be also done easily by hand by using as examples the AMBER99sb-ILDN params available in GROMACS
HTH
Stéphane
---------------------------------------------------------------------------------
De : Matthew Fisher [matthew.fisher.stcatz.ox.ac.uk]
Envoyé : mardi 23 octobre 2018 23:10
À : AMBER Mailing List
Objet : [AMBER] Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME
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)
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Received on Wed Oct 24 2018 - 02:00:02 PDT
