Re: I need help with this

From: Richard Wood (
Date: Fri Feb 11 2011 - 06:07:23 CST

Hi Eduardo,

Actually, attach was a bad word.

What I wanted to do and have done was place a small molecule on the surface of a
bilayer by picking where I wanted to put it and doing a docking calculation in
Surflex Dock.

I then wanted to combine these two files and run MD on the complex. However, I
encountered problems generating a psf file using psfgen. So, I combined the two
files as one big pdb file and created a psf using VMD.

Right now, my calculation is running :)

The problem with psfgen was that if I ran my pdb file through it (after
renumbering the POPC residues) the pdb and psf file couldn't be minimized, while
the raw pdb (without the small molecule) could be minimized. I haven't figured
out why that would be.

But anyway, all is fine for now.


From: Cruz-Chu Eduardo Roberto <>
To: Richard Wood <>
Cc: "" <>
Sent: Thu, February 10, 2011 2:51:43 AM
Subject: Re: namd-l: I need help with this

Hi Richard;

Assuming that "attach" means a covalent bond: The safe way to attach one residue
to another is to create a patch in the topology file, and then run psfgen to
generate the bonding terms between those residues. There is a tutorial about
how to create topology files at:



On Feb 9, 2011, at 8:01 PM, Richard Wood wrote:

Hi all,

I'm trying to set up a system where I have a lipid bilayer and I want to
"attach" a small molecule to the surface so I can run dynamics.

I have generated the bilayer using VMD and I have built the small molecule and
have parameters and a topology for it. The problem I am having is in generating
the psf for the total system.

I have the *.pdb and *.psf for the bilayer and I can run that in namd; in fact,
I am minimizing it now as a test. However, when I try to generate a psf file,
because the bilayer is numbered "funny", some residues have the same number and
don't get converted to the new file. If I try to renumber everything by hand,
then it won't minimize (it gets to about 27 steps and then I get "weird numbers"
like -1.

I'm wondering if anyone has encountered this before and what the workaround is.



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