[gmx-users] protonating GLUs
jalemkul at vt.edu
Mon May 30 22:39:37 CEST 2016
On 5/30/16 4:34 PM, Irem Altan wrote:
> Thank you for your reply. I am running MD simulations where the protein heavy atoms are frozen, so the side chain cannot rotate. Is the aminoacids.hdb file the only file that affects to which oxygen the proton is attached?
No, you would have to change the .rtp (types, charges, bonded connectivity) or
just change the atom names in the input coordinate file (much easier).
>> On May 30, 2016, at 3:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 5/30/16 3:40 PM, Irem Altan wrote:
>>> I am trying to add an extra proton to some of the glutamates in my system. I am using pdb2gmx with the -glu flag. When I tell gmx to add an extra proton, what determines which oxygen atom will be protonated? Is it always attached to OE2, as the aminoacids.hdb file suggests? (I’m using amber03) Is there a way to attach the extra proton to OE1 instead?
>> It's defined by the force field. Choice of oxygen for protonating should be irrelevant; the side chain will rotate over time.
>> 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
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>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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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
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