[gmx-users] No topology

[David van der Spoel]

Edgar Mixcoha Hernández wrote:
> I just want to generate the topology of one protein with water. 
> Previously I had obtained the archive .gro from a .pdb, I used editconf 
> to make a box after I used genbox to add waters to protein. The archive 
> .gro is generated but I have tried many times and with other proteins 
> and I can't generate the archive .top
> 
> I am using the correct command: genbox -cp protein.gro  -cs spc216.gro 
> -o proteinw.gro -p proteinw.top
> 
pdb2gmx


> The error that I recive is:
> 
> 
> *Processing topology
> -------------------------------------------------------
> Program genbox, VERSION 3.3.1
> Source code file: futil.c, line: 340
> 
> File input/output error:
> proteinw.top
> -------------------------------------------------------
> *
> 
> I will thank if someone can help me.
> 
> 
> -- 
> Edgar Mixcoha Hernández, Chemist, BSc
> Laboratorio de Bioquímica, Edificio de Posgrado
> Escuela Nacional de Medicina y Homeopatía, IPN
> Lab +52 55 5729 6000 ext 55562
> Mobile +52 55 2955 2219
> ______________________________
> 
> 
> ------------------------------------------------------------------------
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-- 
David.
________________________________________________________________________
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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