[gmx-users] Force filed for phosphorylated residues

[Mark Abraham]

Hi,

It might be easier to help you with all four of the things I asked you
about.

Mark

On Mon, 12 Dec 2016 17:26 Seera Suryanarayana <palusoori at gmail.com> wrote:

> Dear Mark,
>
> 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
>
> [ impropers]
>
>  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
> Surya
>
>
> Hi,
>
> 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?
>
> Mark
>
>  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?
>
> Surya
> Graduate student
> India.
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