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

[YanhuaOuyang]

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? 
> 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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