[gmx-users] Force filed for phosphorylated residues

[Amir Zeb]

sorry, the ff is charm36 and charm26 is miss typed

On Sun, Dec 11, 2016 at 11:15 PM, Amir Zeb <zebamir85 at gmail.com> 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?
>
> 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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>
>