RE: generating psf files (and more!)

From: Luis Rosales (
Date: Tue Sep 14 2004 - 17:40:20 CDT

Hi Matt!!!

Do you have visited the Hetero-compound Information Centre at Uppsala ???
You can get coordinates for ligands, obtained from the PDB, and you can get
your PDB of interest as a HETATM or an ATOM PDB file,
Also, you can download dictionaries/topology files for Xplor...

As for the CHARMM empirical forcefields, the version C31B1 is available at:
( have links to more topology/parameter
files, under the CHARMM info menu...

Hope this helps,


-----Mensaje original-----
De: [] En nombre de
Enviado el: Martes, 14 de Septiembre de 2004 16:53
Asunto: namd-l: generating psf files (and more!)


I am pretty new at this and I have a couple of questions - any help would be

great - I have looked everywhere for this info but I am lost.

Basically I need to make a .psf file of NAD to run a MD simulation in NAMD.
have the NAD pdb file which I have taken from the PDB file 1QLH.

Question 1: How can I get VMD/NAMD to recognize the atom types in NAD? The
file gives the atoms types with HETATM prefixes, so NAMD thinks that NAD is
all "A" and "N" atoms:
HETATM 2790 AO1 NAD A 377 13.310 6.257 26.771 1.00 72.62
         This causes NAMD to get confused about the connectivity.

Question 2: How do I generate a proper psf file. When I use the following
(which I stole and adopted)... :

package require psfgen
topology ".\\working\\ligand_test\\top_all27_prot_na_qm.inp"
segment U {pdb ".\\working\\ligand_test\\NAD_from_xplor.pdb"}
coordpdb ".\\working\\ligand_test\\NAD_from_xplor.pdb" U
writepdb ".\\working\\ligand_test\\NAD_updated.pdb"
writepsf ".\\working\\ligand_test\\NAD_updated.psf"

... on the NAD pdb file it runs fine but when I load the updated pdb file
loads a crazy looking file with confusing connectivity. I am afraid that
is because I am using a CHARMM topology file that is too complicated for
I want to do - I cannot find any others though.

Question 3: Is there a way to make or find CHARMM topology files for
that are not amino acid based?

I have also used the PRODRG server to make X-plor topolgy files but I cannot

figure out how to use those files with freeware (I do not have access to
programs that cost money) and PRODRG does that thing where it changes the

Question 4: Is there someway to use the X-Plor topology and parameter files
help me out.

I am sorry for the long question - I don't want to mooch so if you even have
link to a good website that will be appreciated - I have been thrown into
deep end a bit on this one and I want to figure this out asap.



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