[gmx-users] Adding hydrogen atom to specific Glu/Asp carboxyl oxygen atom
jalemkul at vt.edu
Wed Nov 9 13:49:35 CET 2016
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.
> 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,
>>> Gromacs Users mailing list
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>> Gromacs Users mailing list
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
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
More information about the gromacs.org_gmx-users