[gmx-users] Force filed for phosphorylated residues
palusoori at gmail.com
Mon Dec 12 07:26:14 CET 2016
I have used the charm36 force field. In c.tdb following atoms are there.
; CHARMM CTER
[ COO- ]
[ replace ]
C C CC 12.011 0.34
O OT1 OC 15.9994 -0.67
OXT OT2 OC 15.9994 -0.67
[ add ]
2 8 OT C CA N
OC 15.99994 -0.67 -1
C CA OT2 OT1
and in rtp file for GLN with other atoms they mentioned only one 'O'
atom. They didn't give the terminal O atom information.
Kindly tell me how to overcome this problem.
Thanks in advance
What atoms do you have in that residue, what's in the c.tdb and .rtp for
GLN in force field and what did you choose for termini?
I have one protein with phosphoserine and phosphothreonine. I want to
do simulation, but I do not know which force field I have to use. None
of the force field from gromacs has the information of phospho
residues. Then I tried with charm36, but did work. Kindly suggest me
what I can do.
Well, CHARMM36 has everything you need included, so unless you explain
what "didnot work" means (because it's the single most useless phrase
anything), there's little anyone can do to help you. Please describe
exactly what the problem was (commands, output, errors, etc).
I solved the problem. That is only the mismatching of residue names
and I renamed the residues in my PDB file. Now the problem is with OXT
atom at C-terminal end.I other words the exact error is "Atom OXT in
residue GLN 68 was not found in rtp entry GLN with 17 atoms while
sorting the atoms ". I understood the error. rtp file does not have
the atom OXT information. How could one solve this problem?
More information about the gromacs.org_gmx-users