[gmx-users] gromos53a6_lipid.ff/forcefield.itp not found
jalemkul at vt.edu
Wed May 27 22:34:33 CEST 2015
On 5/27/15 1:50 PM, Poncho Arvayo Zatarain wrote:
> Hello i'm doing a simulation and when i use grompp grompp -f dppc128.mdp -c dppc128_40ns.pdb -p dppc128.top -o dppc128_1.tpr i have this: Fatal error:
> Topology include file "gromos53a6_lipid.ff/forcefield.itp" not found. What should i include in my topolofy files?
So the force field doesn't exist. Either grompp can't find the
gromos53a6_lipid.ff directory or it doesn't have forcefield.itp (which would
indicate it hasn't been constructed properly).
> And i have 2 notes: NOTE 1 [file dppc128.mdp, line 34]:
> dppc128.mdp did not specify a value for the .mdp option "cutoff-scheme".
> Probably it was first intended for use with GROMACS before 4.6. In 4.6,
> the Verlet scheme was introduced, but the group scheme was still the
> default. The default is now the Verlet scheme, so you will observe
> different behaviour. Should i inlude Cutoff-scheme verlet in my mdp file?
> NOTE 2 [file dppc128.mdp]:
> The Berendsen thermostat does not generate the correct kinetic energy
> distribution. You might want to consider using the V-rescale thermostat. Should i include Berendsen at my Tcouple option on mdp file?
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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