Re: basic pdb file run with namd and vmd

From: J T (jtibbitt_at_odu.edu)
Date: Wed May 23 2007 - 21:49:02 CDT

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Try the tutorials on the VMD and NAMD website. The first VMD
tutorial is good and will show you how to solvated your pdb.

Jeff

On May 23, 2007, at 5:05 PM, Kayode Karunwi wrote:

> Hi everyone,
>
> I'm new to using namd and tried practicing on some small pdb file,
> alanine. This is most likely easy for everyone on this forum.
>
> How do you solvate this molecule and optimize it's energy so it's
> enclosed in a water sphere? Attached are the files I modified but
> feel free to start with the original pdb file, run through and send
> back to me at k.karunwi_at_gmail.com
>
> Thanks in anticipation of your help.
>
> Kayode
>
>
> <alanine.pdb>
> <alanine.pgn.txt>
> <alanine2.pdb>
> <alanine2.psf>
> <alanine2_wb.pdb>
> <alanine2_ws.pdb>
> <wat_sphere_alanine.tcl.txt>

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