Re: I need help with this

From: Cruz-Chu Eduardo Roberto (
Date: Thu Feb 10 2011 - 02:51:43 CST

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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