[gmx-users] Gromacs under Windows

[David]

On Mon, 2004-01-26 at 17:13, Cornel, J. wrote:
> 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,
grompp -p aki


> 
>  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.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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