[gmx-users] Gromacs under Windows

[Cornel, J.]

hoi Anton,

onderaan de aki.top file staan inderdaad die regels die je noemt. 
En ik ben er zeker van dat cpp in

> cpp		= C:\Gromacs\bin\cpp	; Preprocessor

Staat. Echter als ik grompp run met -pp ipv -p dan krijg ik:

Fatal error. topol.top  does not exist,

 en dit betekent neem ik aan dat ie aki.top niet kan vinden, waar kan dit aan liggen??

ook de aki.top file heb ik volgens mij goed gedefinieerd ik minim.mdp

groetjes Jeroen


-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Anton Feenstra
Sent: Monday, January 26, 2004 7:40
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Gromacs under Windows


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)                               |
|_____________|_______________________________________________________|


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