Re: psf generation for a small non-peptide molecule - again

From: Floris Buelens (
Date: Thu Oct 02 2008 - 09:57:49 CDT

Hi Vlad,

I would strongly recommend the generalised amber force field (GAFF) if you don't want to get involved in any ab initio parameterisation. Everything you need is now available as free software under GPL at - you'll need to install that, assign parameters and charges with antechamber, and generate an amber format topology / parameter file, which can be read directly by NAMD.
best of luck,


----- Original Message ----
From: CHINDEA Vlad <>
To: NAMD list <>
Sent: Wednesday, 1 October, 2008 22:38:27
Subject: namd-l: psf generation for a small non-peptide molecule - again

Hi Peter

While runing AutoPSF on the molecule a set of atoms are labeled as unparametrized and PSF generation is stopped. I have used topology file top_all27_prot_lipid since this was provided with the tutorial.

Atom types were set manually in PDB according to the definitions provided in the topology file: for example for an oxygene in a hydroxyl group I have set atom type no. 73 'OH1' which is described in the topology file as 'hydroxyl oxygene'. Isn't this a correct procedure ?

Of course for molecular groups which are missing from peptides it is hard to find the corresponding type: for example for an ether oxygene I have used, as a first trial, the closest type that I could find which was no. 74 'OS' , 'ester oxygene' which is of course not entirely correct. What is interesting is that not only these 'approximately defined atoms' are giving problems in PSF generation but also other atoms which were straightforward to set.

Is there maybe a more general topology file available for non-peptide molecules that I could use ? I would investigate this possibility before attacking the seemigly daunting task of parametrizing a new molecule.

BTW in variouse parts of the documentation I saw top_all27_prot_lipid (CHARMM22) being referred as either a 'force field parameter file' or a 'topology file'. Are these definitions interchangeble or am I missing something ?

Many thanks for your support

All the best

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