[gmx-users] GROMACS compatible Charmm36 Phospho residues

[Parker de Waal]

Thanks Jason for the quick reply,

However I'm a bit concerned about the residue geometry (http://i59.tinypic.com/tar8m9.png), It looks as if the O3P atom is too far from the phosphate group.

Is this normal for SP2 residues in CHARMM?

Best,
Parker

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Wednesday, October 21, 2015 5:34 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] GROMACS compatible Charmm36 Phospho residues



On 10/21/15 5:31 PM, Parker de Waal wrote:
> Hi Everyone,
>
> I'd like to use the phosphoserine/threonine parameters from http://secure-web.cisco.com/1saPOgQehzsBQpgCtRcVZ0er1CHC8XN0-XXMbX33N-se1aJpI-BBhifxulmxh-rYjfzeN1Ar8t-cM8J-Ma-VoewjHW1TJ-6nJYzz5xSffpwMDhRHsu1lzS89MoUvhVAUD4GukIo6gHB5gBj4UP5sQXxSD1sH1g91mHSmIrBl9p3FAagqF8_0vpNoXND7v6w6x-v1ff8MGRNdhxUwx9kGBX259Vjj9rXLgIFUsdAwg0Vw/http%3A%2F%2Fmackerell.umaryland.edu%2Fcharmm_ff.shtml, however it isn't obvious how to apply these without manually editing the charmm36 forcefield files.
>
> Does anyone know the proper way incorporate these paramters/have already done this and would be willing to share?
>

All phosphorylated residues are already present and ready for use.  You just need to add them to residuetypes.dat before running pdb2gmx.

; monoanionic phosphoserine
[ SP1 ]
; dianionic phosphoserine
[ SP2 ]
; monoanionic phosphothreonine
[ THP1 ]
; dianionic phosphothreonine
[ THP2 ]
; monoanionic phosphotyrosine
[ TP1 ]
; dianionic phosphotyrosine
[ TP2 ]

-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://secure-web.cisco.com/1KveaB9Rl5AM5TX1_pOXA_Ui7LZ887V-zeeQx8585AFt-kbWTJkUzhW2q93y8Uu21MViyK9TyDg32QCEXSNcq0yd5CkseEdtE5EvzwAelKQZoarVNsQV7J_eMhnIxOG20YApqVJ8GDsEDrbn4kkRxxZq7WMmkpO8ncyPFdx_wJ0-6-0dIv3bOWbW5o0lbCJEgH0ILUqAX7EZ4_brwX2p0bhptt5aQNz9lIy-mYLEcgZU/http%3A%2F%2Fmackerell.umaryland.edu%2F%7Ejalemkul

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