[gmx-users] Force field for phosphorylated residues

[Seera Suryanarayana]

Dear gromacs users,

 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
in debugging
anything), there's little anyone can do to help you.  Please describe
exactly what the problem was (commands, output, errors, etc).

-Justin



Dear Justin,

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?

Thanks in advance

Surya
Graduate student
India.