[gmx-users] Strange output with Genbox

[David van der Spoel]

Jens Pohl wrote:
>> -----Ursprüngliche Nachricht-----
>> Von: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Gesendet: 13.02.08 14:27:25
>> An: Discussion list for GROMACS users <gmx-users at 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
> _____________________________________________________________________
> Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen!
> http://smartsurfer.web.de/?mc=100071&distributionid=000000000066
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++