[gmx-users] gromacs energy minimization fatal error: Invalid bond type 1000 in constant-PH MD
jalemkul at vt.edu
Wed May 25 13:05:09 CEST 2016
On 5/25/16 6:06 AM, Wang Tao wrote:
> Hi,every one!
> I'm using opls aa in gromacs to conduct constant-PH MD. In my system,PH is equal to 13.There are three kind of groups, NA+,OH- and H2O. The itp file for OH- is created by myself.
This is not what constant pH MD is. You've got a fixed protonation state with
OH- floating around, which may not be physically realistic.
> After having finished the genbox and genion steps sucessfully, i met a problem in energy minimization step. The output information says:Invalid bond type 1000. But i don't really understand what the exact problem is.
> Tried to remove bond definition in itp file for OH-, don't work.
> Tried to remove bond definition in ffbonded.itp for OH-, don't work.
> Replaced OH- with CL-,error infomation disappeared.
> I believe the problem is related to OH- force field parameters,but don't know how to deal with it.
You haven't provided us with its topology, so there's nothing anyone can do but
guess haphazardly. But if removing it solves the problem, you know exactly
where the issue is.
> Can anyone help me?
> Tao Wang
> Thank You!
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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