Re: Psfgen - bonding terms involving disulfide bridges

From: Jérôme Hénin (
Date: Fri Oct 04 2013 - 06:55:47 CDT

Hi Reza,

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
> ( 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?
> Thanks,
> Reza

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