[gmx-users] some question about REMD

[Justin Lemkul]

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 
uses.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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