[gmx-users] gibbs calculation
jalemkul at vt.edu
Sun Apr 8 17:12:34 CEST 2018
On 4/8/18 6:56 AM, Raag Saluja wrote:
> I was calculating the Gibbs' free energy of the tubulin heterodimer and
> gave the command:
> gmx grompp -f /Applications/md/tutorial/gibbs/MDP/EM/em_steep_0.mdp -c
> /Applications/md/tutorial/gibbs/1TUB_solv.gro -p
> /Applications/md/tutorial/gibbs/topol.top -o min0.tpr
> I got this error:
> WARNING 1 [file topol_Protein_chain_A.itp, line 2]:
> Too few gb parameters for type "
> Couldn't find topology match for atomtype "
> Abort trap: 6
It looks like you're trying to do some kind of implicit solvent
calculation and you've got a mangled topology or force field file.
You're looking for some nonsensical atom type within the GB parameters.
If "em_steep_0.mdp" is derived from the approach used in my tutorial, I
don't really follow what you're doing. Alchemical transformations of
proteins are wildly unlikely to succeed, and I don't understand the use
of implicit solvent in this context. If you're trying to do some sort of
MM/PBSA-type calculation, you're going about it incorrectly.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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