[gmx-users] gibbs calculation

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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