Putting multiple copies of peptide in a box

From: Aditya Ranganathan (aditya.sia_at_gmail.com)
Date: Tue Feb 17 2015 - 03:39:14 CST

Dear All,

I have been working on simulating a protein aggregation related problem
using NAMD. In order to do the same, I need to start with multiple copies
of a peptide in the solvent box.

Currently, I do it manually using Chimera or DS Visualizer. However, it is
cumbersome to do so if there are more than 100 or so copies of the peptide
to start with. I`m aware that LAMPPS has a feature where one can repeat
structures in the simulation box.

Are there any vmd scripts that enables one to randomly place multiple
copies of a peptide in the solvent box? Please let me know if there are any
already available to achieve the above.
Thanks and Regards

Srivastav R
Senior Research Fellow,
IIT Bombay

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