[gmx-users] More solvent errors!!!

[Anton Feenstra]

David wrote:

> On Mon, 2003-12-01 at 17:01, Raj Badhan wrote:
> 
>>Dear David,
>>This may be indeed true (sadly!!!), but then why can I seem to run 
>>this when I dont have the ligand (all the way to a full md sim.) but 
>>as soon as I add the ligand using the drug-enzyme tutorial the error 
>>appears?
> 
> 
> could be PBC, check your coordinates. It is definitely in the input
> coordinates of the complex. Check them with a text editor, rather than a
> pdb viewer or something like that.

Have you checked the *actual* box dimensions in your input file to
genbox. I mean, not check the parameters/options you gave to editconf,
but check the contents of the output file (.pdb or .gro) from editconf?
My guess is you ATP is far away from the rest of the system, leading
editconf to define a really big box, which genbox (or, rather, your
computer) cannot handle, and which I think is also not what you intended!


-- 
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)                               |
|_____________|_______________________________________________________|