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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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