[gmx-users] force filed parameters for phosphoserine with gromaces

[Justin Lemkul]

On 6/2/16 9:59 PM, YanhuaOuyang wrote:
> What you mean is that I can use the AMBER parameters on the website (http://sites.pharmacy.manchester.ac.uk/bryce/amber <http://sites.pharmacy.manchester.ac.uk/bryce/amber>) and need to convert the format of the parameters to the one that GROMACS is compatible with in the .rtp entries?

Yes.

-Justin

>> 在 2016年6月3日，上午5:50，Justin Lemkul <jalemkul at vt.edu> 写道：
>>
>>
>>
>> On 6/2/16 10:55 AM, YanhuaOuyang wrote:
>>> Dear Gromacs users,
>>>
>>> I am going to run a MD of a 20-residue protein which is phosphorylated on the
>>> Serine and Threonine residues with AMBER ff99SB-ILDN force field using
>>> Gromacs5.0. When I run gmx pdb2gmx and choose AMBER ff99SB-ILDN force field,
>>> it appears: fatal error: residues SEP not found in residue topology
>>> database.
>>>
>>> I search some papers, and they say that we need to add add force fields
>>> parameters for the phosphorylated amino acids to the force filed parameter
>>> files. But I do not know how to add force fields parameters for the
>>> phosphorylated amino acids. Could anyone knows how to construct a model for
>>> the phosphorylated protein?
>>>
>>
>> AMBER parameters are already available:
>>
>> http://sites.pharmacy.manchester.ac.uk/bryce/amber
>>
>> You just need to convert the format and build suitable .rtp entries.  Or find a force field that already has this done for you (CHARMM36, Gromos96 43a1p, etc).
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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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>

-- 
==================================================

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

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