jalemkul at vt.edu
Tue May 24 16:42:57 CEST 2016
On 5/24/16 10:36 AM, Karina wrote:
> I am trying to restrain the angle between two atoms (type a5) in a half
> spherical body with respect to the z axis. I am trying to use
> angle_restraint_z, but not sure how to do it correctly due to lack of
> information in the manual or in forums.
> I have created a .itp file with angle_restraint_z and included it in the
> topology file as follows:
> #include "a5.itp"
> #ifdef ANGRESZ
> #include "angrez-a5.itp"
> and in the .mdp file as follows:
> define =-DANGRESZ
> The problem is I get the following error
> Fatal error:
> [ file angrez-a5.itp, line 5 ]:
> Atom index (3384) in angle_restraints_z out of bounds (1-1).
> This probably means that you have inserted topology section "angle_restraints_z"
> in a part belonging to a different molecule than you intended to.
> In that case move the "angle_restraints_z" section to the right molecule.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> The only way I can run it is if my indexes are 1 in my .itp file:
> [ angle_restraints_z ]
> ;i j funct theta0 fc mult
> 1 1 1 90 100000 1
> which is incorrect.
> Can you please help me understand how to do it correctly?
Angle restraints are like any other restraints and are numbered based on
[moleculetype] number, not global atom number:
Likely you've inserted your #include statement after your #include
(whatever).ff/ions.itp" or something similar that has only 1-atom [moleculetypes].
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