[gmx-users] pdb

Dinesh Pinisetty dpinis1 at lsu.edu
Wed Jul 14 04:38:51 CEST 2004

Hi everyone,
           I have taken one molecule with 23 atoms from a pdb file of
Glycerol and have written a code in such a way that it translates into
multiple molecules.I have created 8 molecules and then run md
simulations.When I run the mdrun finally it run but at the end it is
displaying step9.pdb,step8.pdb etc.When I checked with ngmx just for
molecules it was not in the box but again when I used genbox and added
water molecules I got the molecule in center with water molecules around
but when I tried to animate it was not working,I think it did not run the
simulation.Is it the problem with the pdb file I am using, as the
co-ordinates are just translated in one direction.Is it the indication that
when simulation did not run properly that we get step7.pdb ,step8.pdb
etc.Now with this problem how can run the simulation,Can anyone help me in
getting pure Glycerol pdb file with residues in residue data
 please let me know this.
Thanks in advance.......

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