<pre><tt>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
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><br></tt></pre><p> 
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