[gmx-users] Amber03 parameters for PTR

[Justin Lemkul]

On 10/14/15 5:52 AM, Amali Guruge wrote:
> Dear Prof. Justin,
>
> Thank you for the reply. Yes, I can use the parameters defined in that
> site, but I have to define the aminoacids.hbd file as well for PTR. How can
> I get that part?
>

Read the manual, and copy most of the existing entry for TYR.

-Justin

> Thank you.
>
> On Wed, Oct 14, 2015 at 3:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/14/15 5:02 AM, Amali Guruge wrote:
>>
>>> Dear All,
>>>
>>> I want to do a molecular dynamic simulation for pdb ID 1K4T crystal
>>> structure using Amber03 force field. The structure contains
>>> phosphotyrosine
>>> (PTR). But parameters for PTR is not available in aminoacids.rtp file.
>>> Therefore can anyone help me to solve my problem.
>>>
>>>
>> http://sites.pharmacy.manchester.ac.uk/bryce/amber
>>
>> -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

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