[gmx-users] Drug - Enzyme tutorial

[Anton Feenstra]

Dastmalchi wrote:
> Dear Collegues,
> 
> I am new to GROMACS, and was going through the Drug-Enzyme tutorial. I am using
> CROMACS on a PC running WinXP. When I issue the following command
> "genbox -cp trp.gro -cs spc216.gro -o trp_b4em.gro -p trp.top", I get an empty
> trp.top file. I tried to edit the top file using temp.top and did many other
> thing to continue the tutorial but it didn't work. I was wondering if you could
> kindly help me out with this.

Hmm. This probably is a bug (and if so, it's my fault) ;-(

The workaround is simple: do not put the '-p trp.top' on the commandline,
and edit the .top file yourself: it is very easy: Genbox tells
you when if finishes how many waters it has added. Just add a line at the
end of the .top file for that number of water molecules, so the end of your
file would look something like this:
....
[ system ]
protein in water

[ molecules ]
Protein		1
Drug		1
SOL		4125

(your mileage may vary)

-- 
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 chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|