[gmx-users] gibbs calculation

Justin Lemkul jalemkul at vt.edu
Sun Apr 8 17:12:34 CEST 2018

On 4/8/18 6:56 AM, Raag Saluja wrote:
> Hi!
> 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.
Assistant Professor
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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