[gmx-users] protein problem

David van der Spoel spoel at xray.bmc.uu.se
Mon Jun 12 21:32:32 CEST 2006

-------- 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.

I will be glad to hear any comments from you. I am using Gromacs3.3.1 



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

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