From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Oct 04 2013 - 06:55:47 CDT
Most probably, the BPTI example is just old, and wasn't updated to reflect the change from C27 to C3* topology files, where all "generic" angles and dihedrals were removed from PRES entries.
Ever since then, the "regenerate angles dihedrals" command has been necessary after applying patches.
----- Original Message -----
> Hi all,
> I followed the BPTI example in the psfgen manual
> (http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf) and noticed that
> when patching the disulfide bridges, the angle and dihedral terms that
> involve the bridges are not automatically generated (e.g. SG-SG-CB angle).
> This is also the case with AutoPSF.
> I found out that using the "regenerate" command after DISU patches seems to
> generate the missing angles and dihedral correctly. So I'm just wondering if
> the regenerate command is missing from the BPTI example or if it is
> intentionally left out?
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