generating psf files (and more!)

From: mdcooper (
Date: Tue Sep 14 2004 - 16:52:38 CDT


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. I
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 PDB
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 code
(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 VMD
loads a crazy looking file with confusing connectivity. I am afraid that this
is because I am using a CHARMM topology file that is too complicated for what
I want to do - I cannot find any others though.

Question 3: Is there a way to make or find CHARMM topology files for molecules
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 atom

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

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



This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:52 CST