[gmx-users] Constraining hydrogen - heavy atom bonds with different naming.
jalemkul at vt.edu
Tue Mar 1 19:50:00 CET 2016
On 3/1/16 1:42 PM, Dawid das wrote:
> Oh gosh..., so in that case is there any other way around to constraint
> those MH11 - MCB1 etc. bond lengths except for renaming all hydrogen atoms?
Renaming takes approximately one second:
sed -i "s/MH/HM/g" *
(assuming of course that the pattern "MH" is only ever encountered in your
custom H names...caveat emptor).
> Best wishes,
> Dawid Grabarek
> 2016-03-01 19:29 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>> On 3/1/16 1:24 PM, Dawid das wrote:
>>> Dear Gromacs Experts,
>>> I am pretty sure I have already answered this question long time ago but I
>>> cannot find
>>> it. What I did is I added a new residue for my system and it contains
>>> hydrogen atoms.
>>> Now, the thing is that all atoms names start with "M", so I have MH21,
>>> MH22, MCA1, etc.
>>> atoms. I want to constrain hydrogen - heavy atom bonds:
>>> constraints = h-bonds
>>> and I am not sure whether I constraint those novel hydrogens. In other
>>> words, how does
>>> Gromacs 5.0.4 know that my atom is a hydrogen? Based on atomic number in
>>> ffnonbonded.itp or based on atom name/type?
>> It's based on name. If the first character is H, it is added to the
>> constraint list. So your case will not work. You can always confirm what
>> is constrained by using gmx dump on the .tpr file and looking for F_CONSTR.
>> 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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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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