[gmx-users] Force filed for phosphorylated residues

[Justin Lemkul]

On 12/12/16 2:15 AM, Amir Zeb wrote:
> Hello Surya,
>
> 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?
>

"SER" is normal serine.  "SP1" is monoanionic phosphoserine, "SP2" is dianionic. 
  The residue name and the atom names have to match the expectations of the .rtp 
file.  Read it to determine if everything checks out.

-Justin

> Thanks in advance
>
> Amir
>
> On Sun, Dec 11, 2016 at 10:26 PM, 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================