[gmx-users] Hydroxyl bonds rotating too much

Juan José Galano Frutos juanjogf at gmail.com
Tue May 16 16:28:30 CEST 2017

Thank you Justin. The problematic OH is part of the cofactor molecule.
This OH group is located in an extreme part of the cofactor so it
apparently only interacts with solvent, not with the protein.

I'm doing just now some tests of the cofactor solvated in order to
check if the problem comes from the cofactor itself or comes from
other issue.

I'll post here the result of this test whatever it is.

Thank you again.


On 5/16/17 7:03 AM, Juan José Galano Frutos wrote:
>* Hi there:
*>>* I am simulating a protein which include as a cofactor a molecule bearing
*>* some hydroxyl groups. The system is crashing from the begining of the
*>* equilibration step (after the following steps: vaccuum minimization,
*>* solvating, neutralizing, minimization, heating) due to -in all the
*>* replicas- to hydroxyl bonds that steadily rotated more than 60 and even 90
*>* degrees.
*>* I checked the structures and the systems looking for either water or
*>* protein parts in so close contact with this hydroxyl groups, but it was not
*>* the case. Then I proceeded to re-minimize again the systems after the
*>* heating step and afterward to relaunch the equilibration step, but again
*>* the same happened. I also checked the topology file of this cofactor but
*>* all seems to be fine, I mean charges.
*>* Then, what could be happening? Is it common this behaviour in hydroxyl
*>* groups?Any help please....
What does the problematic OH group interact with?  The over-rotation is a
symptom, not a cause.  If it interacts with your cofactor, the parameters for
that cofactor are likely suspect.  Typical diagnostic steps are in



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
<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> |
(410) 706-7441http://mackerell.umaryland.edu/~jalemkul


Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)

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