[gmx-users] genbox failed

[Anton Feenstra]

David wrote:

> On Thu, 2004-09-30 at 23:05, Yunfeng Hu wrote:
> 
>>Hi,  I am using the latest gromacs and compiled without errors. I am 
>>following John Kerrigan's tutorial for drug-enzyme complex. Gromacs 
>>fails at genbox no matter how small the probe is used. Here is a 
>>summary of the commands I use:
>>
>>editconf -bt octahedron -f test.gro -o test.gro -c -d 0.5
> 
> maybe you want to try it with different file names above.
> 
> 
>>genbox -cp test.gro -cs spc216.gro -o test_b4ion.gro -p test.top

Also, the '-p test.top' will cause genbox to read from and write to the
same file. Some OS's may not like that. You can simply omit the '-p' and
add the line 'SOL   #' at the end of the .top file yourself, where '#'
stands for the number of water molecules added (genbox reports that at
the end).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
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