Jens Pohl wrote:
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Von: Discussion list for GROMACS users <gmx-users@gromacs.org>
Gesendet: 13.02.08 14:27:25
An: Discussion list for GROMACS users <gmx-users@gromacs.org>
Betreff: Re: [gmx-users] Strange output with Genbox
Jens Pohl wrote:
Hello!
I try to simulate a modified protein in a water-box. When I use genbox and have a look on the output-file then the water molecules are located in between the AA-sequence which results in an "exploding" molecule during the mdrun. I've done it several times from the very beginning, always getting a similar result (distribution of water in the AA sequence varied a bit).
Input-sequence (AA):
MGVLAI...
Output after genbox:
OMOGOOVOLOAOIOO...
Commands used (copied from .bash_history):
pdb2gmx -f 165_in.pdb -p 165 -o 165 -n 165 -i 165 -q 165_out.pdb
(used ffG53a6)
editconf -f 165 -o CbzE_ec.pdb -bt cubic -vol -d 1.0
genbox -cp 165_ec.pdb -cs ../Water.gro -o 165_gb.pdb -p 165_gb
What is in ../Water.gro? It should be pure water.
Water.gro is my renamed SPC water from the GROMACS package.
What system are you running on?
Simple Pentium IV-system with which I've done some simulations before.
OK, but did you recompile using !"#€%& gcc 4.1.x recently?
Otherwise if this is reproduciible please submit a bugzilla with all
necesary files.
Thank you very much in advance for your suggestions to solve the problem
Jens
Jens
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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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