[gmx-users] some question about REMD

Justin Lemkul jalemkul at vt.edu
Wed Oct 17 20:35:58 CEST 2012

On 10/17/12 2:31 PM, Albert wrote:
> Hello Justine:
> I've got the following messages by command:
>   grompp -f implicit.mdp -c complex.pdb -p complex.top -o test.tpr
> Setting gen_seed to 18463
> Velocities were taken from a Maxwell distribution at 310 K
> GB parameter(s) missing or negative for atom type 'OS'
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: grompp.c, line: 1123
> Fatal error:
> Can't do GB electrostatics; the implicit_genborn_params section of the
> forcefield is missing parameters for 1 atomtypes or they might be negative.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> "Uh-oh .... Right Again" (Laurie Anderson)

You need GB parameters for every atom type in the system.  Most protein and 
nucleic acid types work out of the box, but if you have a complex system with 
some novel molecule in it, you have to add parameters for the atom types that it 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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