issues with AutoPSF for a cyclodextrin

From: CHINDEA Vlad (vchindea_at_hotmail.com)
Date: Thu Oct 29 2009 - 18:32:50 CDT

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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