Re: I need help with this

Date: Fri Feb 11 2011 - 10:35:52 CST


Did you try to make one psf for the system without your small molecule and one with the molecule alone and then combine them in vmd with readpsf?. Later you can delete the water molecules (or whatever was located in the place where you want your ligand) with delatom and write your final psf and pdb files.

----Mensaje original----


Fecha: 11-feb-2011 9:07

Para: "Cruz-Chu Eduardo Roberto"<>

CC: ""<>

Asunto: Re: namd-l: I need help with this

-->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


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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