[gmx-users] Errors about dihidral angle type 9 in free energy perturbation

Justin Lemkul jalemkul at vt.edu
Fri Dec 5 13:35:33 CET 2014

On 12/4/14 9:30 PM, Jianguo Li wrote:
> Thanks Justin for your reply.
> Actually we have modified ffbonded.itp to include the state B parameters for
> dihedral function type 9, but they are not recognized by GROMACS. We did not get
> any error when using gmx4.0.4 and amber99sb, in which dihedral type 3 (RB) is
> used.  We get the error only when we use tpye 9 with multiple terms. But in
> Chapter 5 table 5.5, it is clearly written that type 9 can be used in free
> energy perturbation.

Comparing an old version and a different function type is not applicable :)

Yes, type 9 dihedrals can be perturbed, but you have to do a bit more work 
within the topology for it to work.

> I will try to include the parameters explicitly in the topology file of the
> protein, but it needs some scripting work. Apart from this, is there any other
> way to make it work?

Directly specifying the parameters in the topology is the only way I know of for 
type 9 dihedrals.



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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