[gmx-users] reg grompp error in QM/MM of mopac gromacs

David van der Spoel spoel at xray.bmc.uu.se
Wed Sep 15 08:55:33 CEST 2010

On 2010-09-15 07.55, vidhya sankar wrote:
> Dear sir/Madam  thanks in Advance
> i wanted to do QM/MM for simple peptide .i have edited my topology files
> as given in the manual i also include the Link atom(LA) under [DUMMIES2]
> secction of my topology .but when i run the following grompp command
> ./grompp_d -f em.mdp -c spep_b4em.gro -p spep.top -o spep_em.tpr
> I got the error as follows
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.29#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp

the instructions are outdated. [ dummies2 ] should be replaced by [ 
virtual_sites2 ] (check the manual for exact syntax).

> -------------------------------------------------------
> Program grompp_d, VERSION 4.0.7
> Source code file: topdirs.c, line: 99
> Fatal error:
> Invalid pairs type 0
> -------------------------------------------------------
> the suggestions are highly appericiated

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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