[gmx-users] Force field for phosphorylated residues

Mark Abraham mark.j.abraham at gmail.com
Fri Dec 9 06:14:58 CET 2016


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?


On Fri, Dec 9, 2016 at 4:05 PM Seera Suryanarayana <palusoori at gmail.com>

> 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.
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