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 ______________________________ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php