[gmx-users] pdb

David spoel at xray.bmc.uu.se
Wed Jul 14 08:04:58 CEST 2004

On Wed, 2004-07-14 at 04:38, Dinesh Pinisetty wrote:
> 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
> base...........

If you start by minimizing the energy of one molecule (and verify it
keeps it structure) you can thereafter use genconf to get multiple
molecules, and genbox to solvate them.

>  please let me know this.
> Thanks in advance.......
> Dinesh.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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