[gmx-users] Force filed for phosphorylated residues

Peter Stern peter.stern at weizmann.ac.il
Mon Dec 12 11:04:37 CET 2016


Hi,

Check the documentation:
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Amir Zeb
Sent: Monday, December 12, 2016 9:35 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Force filed for phosphorylated residues

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.
> > --
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