VMD-L Mailing List

From: Guanyu Wang (wangg348_at_myumanitoba.ca)
Date: Thu Apr 06 2017 - 17:46:24 CDT

Hi there,

I am new to VMD and I encountered some problems while using the Autopsf gui. My protein has a structural calcium binding to several residues. When I am trying to generate the psf file using Autopsf, the calcium ion is recognized as AO1. But in the final output, calcium is placed in the origin instead of where it should be. I was trying to patch the calcium ion to one of the residues. However, it gives the error message "psfgen) unknown patch type AO1:1". Is there any specific instructions I need to follow in order to include the calcium in the final output file? I would really appreciate it if someone could help me!

And by the way, in the 1.9.3 Mac OS X X86 version of VMD, the topology file " top_all36_carb.rtf" renames NAG as BGLCNA. However, the "autopsf.tcl" renames NAG as BGLN. This causes autopsf to stop running because it cannot find BGLN in the topology file. This can be fixed by changing BGLCNA to BGLN in the topology file. I hope this can help someone with the same problem.

Cura, ut valeas!
Guanyu Wang