[gmx-users] Protein is out the box

Edgar Mixcoha Hern=?ISO-8859-1?B?4Q==?=ndez edgarmixcoha at gmail.com
Wed Jun 14 00:01:11 CEST 2006

I want to make a molecular dynamic with a protein, I make the .gro and .top
with pdb2gmx, after I put the protein inside a box with editconf, I put
water to the box with genbox, I check the archive in VMD and protein is
inside together with waters molecules.
When I execute grompp to make to get the .tpr file and I feed it to mdrun I
get an archive trr and other gro with the coordinates of my protein. I
visualize the archive gro and the trayectory with VMD and my protein is out
the box, and the water is inside it, I can see the shape of the protein
arounded with water molecules but is out.
What can I do?

In the other hand, I work with a Powerbook I get install GROMACS but grompp
doesn't work, for all proteins gets out an error.

Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (Msaab3-1w.gro, 27339)
             does not match topology (Msaab3-1.top, 0)

But when I check the topology and the gro archive, both are Ok..
And allways says that topology archive have 0 coordinates

I'll thank for help... I need to finish it to graduate...

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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