[gmx-users] problem using makehole program

nur avneet nuravneet at yahoo.co.in
Wed Dec 12 11:30:31 CET 2007

Dear All
i started makehole program...but am facing problems setting
the  mdp parameters.

when i gave mdrun command i get an error..that i cant make out:
the command i gave is:- 
/usr/local/gromacs/i686-pc-linux-gnu/bin/mdrun -v -hole -holep hpgr.mdp -s dmpc_water_1ns.tpr -o cecmel311334_dmpc_hole_1ns.trr -c cecmel311334_dmpc_hole_1ns.gro -e cecmel311334_dmpc_hole_1ns.edr -g cecmel311334_dmpc_hole_1ns.log

> WARNING 1 [file , line 1]:
>   Unknown left-hand molsurf_log in parameter file
> Reading ASCII grasp surface
> atomic surface: allocating list of nn vertex of each
> of 16853 atoms 
> atomic surface: reading surface data from file
> grasp_sur_ascii
> atomic surface: reading 6712 vertices and normals
> and
> 13420 triangles...done
> Back Off! I just backed up gsurf.log to
> ./#gsurf.log.1#
> starting mdrun 'dmpc $ 3655 water in constant
> 0.596'
> 500000 steps,   1000.0 ps.
> Back Off! I just backed up
> cecmel311334_dmpc_hole_1ns.trr to
> ./#cecmel311334_dmpc_hole_1ns.trr.2#
> Back Off! I just backed up insidesurf.pdb to
> ./#insidesurf.pdb.2#
> Fatal error: Don't worry, this is in fact a normal
> stop in debugsurf mode: 
> now check insidegr.pdb and molsurfpdb.pdb
And when i try to open molsurfpdb.pdb...vmd shows
error, that no of bonds is too much. so the file
doesnt open. and 'insidegr.pdb' named file is not formed in my directory.

please guide me through....

I am attaching the *.mdp file with this mail. 


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