[gmx-users] Grompp error while using dual topology for free energy

[bipin singh]

Thanks Dr. Justin for the reply. I have figure out the problem.


On Fri, Nov 22, 2013 at 2:59 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On Thu, Nov 21, 2013 at 4:27 PM, bipin singh <bipinelmat at gmail.com> wrote:
>
> > Hi all,
> >
> > For calculating the free energy of solvation, I have defined the end
> states
> > in the topology file.  But while executing grompp, it displays the error:
> >
> > Program grompp_mpi, VERSION 4.6.3
> > Source code file: /sw/source/sandbox/gromacs-4.6.3/src/kernel/grompp.c,
> > line: 518
> >
> > Fatal error:
> > No molecules were defined in the system
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> >
> >
> > *mdp settings for free energy:*
> >
> > free-energy              = yes
> > sc-alpha                 = 0
> > sc-power                 = 1
> > sc-r-power               = 6
> > init-lambda-state        = 0
> > fep-lambdas              = 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9
> 1.0
> > coul-lambdas             = 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9
> 1.0
> > nstdhdl                  = 100
> > dhdl-print-energy        = yes
> >
> >
> You forgot the couple-moltype keyword, so grompp has no idea what you're
> transforming.
>
> -Justin
>
> --
>
> ==========================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
>
> ==========================================
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-- 


*-----------------------Thanks and Regards,Bipin Singh*