[gmx-users] Force filed for phosphorylated residues

[Amir Zeb]

thanks to all of you for your advice

amrir

On Mon, Dec 12, 2016 at 4:04 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
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