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the instructions are outdated.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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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