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

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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