Dear All<BR>i started makehole program...but am facing problems setting<BR>the mdp parameters.<BR><BR>when i gave mdrun command i get an error..that i cant make out:<BR>the command i gave is:- <BR>/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<BR><BR>> WARNING 1 [file , line 1]:<BR>> Unknown left-hand molsurf_log in parameter file<BR>> <BR>> Reading ASCII grasp surface<BR>> atomic surface: allocating list of nn vertex of each<BR>> of 16853 atoms <BR>> atomic surface: reading surface data from file<BR>> grasp_sur_ascii<BR>> atomic surface: reading 6712 vertices and normals<BR>> and<BR>> 13420 triangles...done<BR>> <BR>> Back Off! I just backed up gsurf.log to<BR>> ./#gsurf.log.1#<BR>> starting mdrun 'dmpc $ 3655 water in
constant<BR>area<BR>> 0.596'<BR>> 500000 steps, 1000.0 ps.<BR>> <BR>> <BR>> Back Off! I just backed up<BR>> cecmel311334_dmpc_hole_1ns.trr to<BR>> ./#cecmel311334_dmpc_hole_1ns.trr.2#<BR>> <BR>> Back Off! I just backed up insidesurf.pdb to<BR>> ./#insidesurf.pdb.2#<BR>> Fatal error: Don't worry, this is in fact a normal<BR>> stop in debugsurf mode: <BR>> now check insidegr.pdb and molsurfpdb.pdb<BR>> <BR>And when i try to open molsurfpdb.pdb...vmd shows<BR>error, that no of bonds is too much. so the file<BR>doesnt open. and 'insidegr.pdb' named file is not formed in my directory.<BR><BR>please guide me through....<BR><BR>I am attaching the *.mdp file with this mail. <BR><BR>regards<BR>nur<BR><p> 
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