Dear all,
I have a phosphorylated protein (1 phosphorylated amino acid) for MD simulation, using the Amber parm99sb force field ported in gromacs via amberports. I found the Amber ff parameters for phosphorylated amino acids (J Mol Model 2006, 12;281-89) providing both the frcmod and lib files.
I have manually introduced the new residue type and the charges into the gromacs residue topology file, but my concern is transferring the force constants for the bonded parameters.
It is my understanding, that I can not simply use the original Amber parm99sb force constant within the amberport as if it was in Amber suite of programs.
Could you please advise me on how to go about the force constants in amberports?
Any suggestion will be greatly appreciated,
best regards
Jarmila
Jarmila Husby, PhD Candidate
CRUK PPI Drug Discovery/ BMSG Group
Department of Pharm & Biol Chemistry
The School of Pharmacy, University of London
email: jarmila.husby.live.pharmacy.ac.uk
tel: (44) 0207 753 5996
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Received on Mon Dec 06 2010 - 06:30:03 PST
