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

Jianguo Li ljggmx at yahoo.com.sg
Fri Dec 5 03:44:34 CET 2014

 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. 

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?

     On Thursday, 4 December 2014, 20:55, Justin Lemkul <jalemkul at vt.edu> wrote:


On 12/4/14 2:32 AM, Jianguo Li wrote:
> Dear All,
> I am trying to use free energy perturbation module of gromacs to do hamiltonian replica exchange using CHARMM27 all-atom force field (with CMAP) - version 2.0
> I am using 4.5.4 version of gromacs
> according to manual (Table 5.5), it allows to perturb dihedral angles: proper dih. multi,  ftp 9, phi and k are allowed under 'F.E.'
> I have edited charmm files( ffbonded.itp and also ffnonbonded.itp) for "state B" parameters.
> but when I run simulations, it throws following error (for 23 lines):
> "
> ERROR 1 [file topol-edited-charmm.top, line 1453]:
>    Cannot automatically perturb a torsion with multiple terms to different
>    form.
>    Please specify perturbed parameters manually for this torsion in your
>    topology!
> "
> What is the fix for this?
> Why gromacs is not recognising the 'state B' parameters?

Because you haven't supplied any.  In this case, you need to explicitly write 
state A and B parameters in the topology.


> I also tried to do this with higher version of gromacs (including latest). It throws the same error.
> Thank you very much for your time.
> Cheers,Jianguo


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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