[gmx-users] phosphotyrosine peptide
farial.tavakoli at ymail.com
Tue Apr 24 07:44:01 CEST 2018
Dear GMX users
I performed a simulation on the complex composed of a protein and a peptide which has 2 residues phosphotyrosines using charmm36 force field in GROMACS. After that I used g_mmpbsa to calculate the binding energy and energy contribution per residue , but the binding energy was calculated + 426 kj/mol. I sent an email to gmmbsa mailing list and informed them , but they replied :" we have not tested the g_mmpbsa with charmm36 so we can't say about the validity. Other members of g_mmpbsa tool, also previously reported about the positive binding energy when using charmm36 force field." in fact they couldnt help me. as they noticed , it is because of using charmm36 ff. Is there anyone can help me which force field I should use in gromacs till I wont have any problem when I am going to use g-mmpbsa ?
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