[gmx-users] Force filed for phosphorylated residues

[Amir Zeb]

Hello Mark,

Please help me for this issue

I want to simulate a protein where ser is phosphorylated. i used charm26 ff
but i m getting this error "Atom P in residue SER 4 was not found in rtp
entry SER with 11 atoms
while sorting atoms". can you please suggest me any possible solution for
this issue?

Thanks in advance

On Sun, Dec 11, 2016 at 11:22 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>