[gmx-users] protein problem

David van der Spoel spoel at xray.bmc.uu.se
Mon Jun 12 21:43:45 CEST 2006

David van der Spoel wrote:
> -------- Original Message --------
> Date: Mon, 12 Jun 2006 16:47:11 +0100
> From: Didier Mu-kindemb <didier.mu-kindemb at kellogg.oxford.ac.uk>
> To: spoel at xray.bmc.uu.se
> Hi David,
> My name is Didier and I am a Bioinformatics student at Oxford 
> university.  I am writing to seek help with Gromacs. I am doing a 
> molecular dynamics of a protein using Gromacs, I am getting an error 
> message and I do not know how to solve it.  From tutorial, I can run 
> pdb2gmx, editconf, and genbox without any error messages but after 
> grompp I am getting an error message saying "number of coordinates in 
> coordinate file (1v4_b4em.pdb, 175038) does not match topology 
> (1v4s.top,0).  Have you got any idea how to solve it, please?  I am 
> thinking of  editing one of those file but I am sure what sort of 
> editing need to be done.

the top file has no atoms. so this is the wrong one.

> I will be glad to hear any comments from you. I am using Gromacs3.3.1 
> version.
> Cheers
> Didier

David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list