[gmx-users] Gromacs under Windows

[Anton Feenstra]

Cornel, J. wrote:

> 
> 
> Hi, 
> 
> I am running Gromacs under Windows 2000 and am reworking the MD course of RUG with the protein lysozyme. The pdb-file was succesfully converted into aki.top and aki.gro but when I try to generate the tpr-file with grompp I get the following error:
> 
> 
> Back off! I just backed up mdout.mdp to ./#mdout.mdp.5#
> Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> checking input for internal consistency...
> calling C:\Gromacs\bin\cpp...
> processing topology...
> processing coordinates...
> Fatal error: number of coordinates on coordinate file <aki.gro,1555>
> 		does not match topology (aki.top,0>
> 
> 
> But I am sure that these numbers are the same 1 protein of 1321 atoms and 78 water molecules (234) is together 1555.

Have you checked your aki.top? Are there lines at the end under the [system]
heading, like this:
---
[system]
protein in water

[molecules]
Protein		1
Sol		78
----

> I also downloaded the minim.mdp file in the MD course and adapted it to my windows system, at least I think I did. It looks likes this:
[...]
> cpp		= C:\Gromacs\bin\cpp	; Preprocessor

Are you sure that is the location of your cpp, and that it actually works?
grompp depends on it, but may not always detect a failure...
Try running grompp with the flag '-pp', that will write the cpp pre-processed
topology file. Check at the end if all things still look as you expect them.

-- 
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)                               |
|_____________|_______________________________________________________|