[gmx-users] to generate phosphotyrosine topology

farial tavakoli farial.tavakoli at ymail.com
Mon Jan 1 11:23:09 CET 2018

Dear gromacs users
I need to generate topology for my protein-peptide complex which the peptide has 2 phosphotyrosine residues. I used CHARMM36 force field to do that. I n that way, I downloaded this force field from http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs and paste it in working directory. Then issued :gmx pdb2gmx -f .pdb -o .gro -water tip4p -ignh  selected charmm36 all-atom force fieldfrom the working directorybut at last faced to this error:
Fatal error:
Atom P1 in residue TYR 3 was not found in rtp entry TYR with 21 atoms
while sorting atoms.

Is there anyone can help me?
best Farial

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