[gmx-users] charmm forcefield patches in gromacs

[Justin Lemkul]

On 3/29/14, 2:22 AM, Gurunath Katagi wrote:
> Dear all,
> I want to do a simulation of protein containing phosphotyrosine using
> charmm forcefield (c32b1). A patch to obtain phosphotyrosine has been
> included in top_all27_prot_na_all.rtf file as TP2 (c32b1/toppar/stream dir).
>
> But i see that, in the aminoacids.rtp this patches havent been included. Is
> there a way to include these patches into this forcefileld and run the
> simulation using gromacs.
> The obvious thing I can do is to add these patches as new residues and so
> on as given in the "how to add a resiude to forcefield ?
> Is there any alternative to include this patches . ?
>

The obvious answer is the right one.

> and also, can gromacs team care of including all other residues in the next
> release.. ?
>

Including all possible residues is a rather tall task and requires a fair bit of 
manual work, especially in the case of patches.  The charmm27.ff files are 
unlikely to change; I will consider adding phosphorylated residues to our next 
release of charmm36.ff, but only as time allows.  In our conversion program, 
dealing with PRES is a pain because the .rtp entries have to be written 
manually, which is not only error-prone but time-consuming.

-Justin

-- 
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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 601
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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