From: Michel Espinoza-Fonseca (
Date: Fri Apr 08 2005 - 12:27:54 CDT

Hi Michael,

I guess what you have to do is very easy. First of all, remove all
hydrogens from your protein using Swiss PDB viewer, for example. Then
save your pdb file WITHOUT hydrogens. After that, use the pdb file
without hydrogens to create your pdb and psf files, using psfgen (psfgen
will add the hydrogens automatically).

If you have further questions, make me know...

I hope it helps,





From: [] On
Behalf Of Michael Grabe
Sent: Friday, April 08, 2005 12:05 PM
Subject: namd-l:


hello all,


i use modeller to produce homology models with hydrogen atoms,

and it seems that the naming convention for the hydrogens

is different from the naming convention used inthe CHARMM files

I use to create the topology files. I use psfgen for this step.

I have tried to use the alias command for some of these but that

is a lot of hydrogens.


has some one compiled all of the correct aliases for the conversion

between these two formats?





Michael Grabe, Ph.D.


Genetics Development & Behavioral Science Building

1550 4th Street, GD 481

San Francisco, CA 94143-0725

tel: ++ 415.476.0421


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