[gmx-users] WARNING: all CONECT records are ignored

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 24 10:46:19 CEST 2006

Joern Lenz wrote:
> dear gromacs guys,
> trying to do some simulations using gromacs i used pdb2gmx as the first step 
> of all of my work.
> i use the following command and the oplsaa forcefield.
> pdb2gmx -ignh -missing -ff oplsaa -f $1 -o $1.gro -p $1.top
> running the pdb2gmx program there always occurs the same warning message:
> Opening library file /home/jlenz/bin/gromacs/share/gromacs/top/ffoplsaa.rtp
> Opening library file /home/jlenz/bin/gromacs/share/gromacs/top/aminoacids.dat
> WARNING: all CONECT records are ignored
> Opening library file /home/jlenz/bin/gromacs/share/gromacs/top/xlateat.dat
> 26 out of 26 lines of xlateat.dat converted succesfully
> All occupancies are one
> .
> .
> .
> How can i fix this warning ? i have no idea. and i want to have this warning 
> fixed before i start the time consuming simulation parts.
> if anyone has an idea, please be so kind and give me a yell.
> otherwise i cannot go on with simulation.
> thanks a lot and have a nice day.

for proteins it will work fine.
for anything else you will have to check your topology.

> greetings
> joern
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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