Hello all, I want to simulate Gamma amino acids using GROMACS, if anybody know where to get the forcefield parameters for gamma amino acids , kindly direct me ..
Thanks in advance.
Dr Zhaoxi Sun Thank you for your reply.
It would be nice if you share your knowledge on how to parameterize non-standard amino acids for AMBER/CHARMM FF. (Swiss Side Chain database seems good for few non-standard ones but it is very limited, plus I feel CGenFF is good for small molecules, alone)
Can you suggest any software to derive Partial Charges, compatible with AMBER/CHARMM FF.
Thanks again.
Dear Vignesh,
The force field parameters for the various kinds of amino acids are available in PTM Vienna server. Just check it maybe you will find the in the follow the link: http://vienna-ptm.univie.ac.at/?page_id=218
Best,
Jamoliddin
Dr. Jamoliddin Razzokov , Thank you for your reply.
PTM Vienna Server seems very interesting, Sir. I will check on this more. But is it compatible with GROMACS v2019?
TIA, Sir
The developed force field parameters can be found in the following link: http://vienna-ptm.univie.ac.at/?page_id=100
You have to download them and copy to the GROMACS database directory.
While you are generating a topology you will choose the appropriate one force field parameters. ffG45a3, ffG54a7 and ffG54a8 united atom GROMOS force field parameters are available in PTM server.
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