VMD-L Mailing List

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Mon Dec 01 2008 - 13:52:31 CST

Hi Dear VMD Users,
I'm now trying to prepare  initial structure ( a pdb file ) and get the prmtop and inpcrd input files for MD simulation in AMBER9 program package. I want to do MD simulations for 500 octane molecules and position molecules in defined regions of space  in   a cubic simulation box. Can I do it and create a pdb file with using VMD ? If it is possible , I would be very grateful if you can help me to learn this operation. I waiting for  the contributions.
 
Thank you very much for your attention.
 
Kind regards