[gmx-users] Adding hydrogen atom to specific Glu/Asp carboxyl oxygen atom

[Justin Lemkul]

On 11/9/16 7:07 AM, Dawid das wrote:
> Yes, I have already figure that out, thanks ;). I have simply exchanged OE1
> and OE2 atoms names and translated HE2 atom by vector between OE1 and OE2
> in *gro file. Also I exchanged OE1 and OE2 atom names in *top file.
>

For future reference, simply switching the atom names and re-running pdb2gmx 
will save you all the manual work.

Note, too, that this is a rotatable bond so if, e.g. a hydrogen bond would be 
favorable, the carboxylic acid group will rotate to form that interaction, 
likely during a simple energy minimization.

-Justin

> Best regards,
> Dawid Grabarek
>
> 2016-11-09 12:56 GMT+01:00 Dd H <ddhecnu at gmail.com>:
>
>> Exchange their atom names？
>>
>> Dading Huang
>>
>> On Wed, Nov 9, 2016 at 7:23 PM, Dawid das <addiw7 at googlemail.com> wrote:
>>
>>> Dear Gromacs Experts,
>>>
>>> I know how to specify which Glu/Asp residues are to be
>>> protonated/deprotonated with
>>> pdb2gmx tool. However, I do not like that the hydrogen is added to one of
>>> the oxygen atoms
>>> of carboxyl moiety. I would like it to be found on the other oxygen. Is
>>> there any other way
>>> except modifying the *top file by hand?
>>>
>>> Best regards,
>>> Dawid
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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

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