Re: issues with AutoPSF for a cyclodextrin

From: Peter Freddolino (
Date: Thu Oct 29 2009 - 19:31:00 CDT

Hi Vlad,
autopsf does not do anything to automatically detect when arbitrary
bonding patches should be applied (which would really be a complex
problem). You can either apply the patches that you need manually
through the patch dialogue, or alter the topology to make those bonds
part of the residue definition.
More information would be required to determine the lack of coordinates
-- were there any warnings or errors while psfgen was running?

CHINDEA Vlad wrote:
> Dear NAMD users
> I am trying to build the PSF of a cyclodextrin starting from an X-ray
> diffraction PDB with a bit of manual adjustment done (file attached).
> I have used topology files top_all22_sugar.inp and/or
> top_all36_carb.inp. When applying AutoPSF the 10 interconnected
> glucose residues were replaced by 10 independent glucose molecules in
> the resulting PSF and PSB although patches for alpha glycosidic bond
> are available at least in top_all36_carb.inp. Also the PDB contains
> only blank coordinates. What would be the reason and what can I do
> about it ?
> I would like to mention that I have changed the name of the glucose
> residue from AGLC to AGL in topology and PDB file as according to my
> knowledge (PDB specs 3.20) residue names should have only 3 characters.
> Many thanks for your support
> Best wishes
> Vlad
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