Angles and dihedral generation

From: Cesar Luis Avila (
Date: Fri Sep 01 2006 - 20:02:36 CDT

Where can I find information on when to generate angles and dihedrals
for different segments?
Throughout internet I have found different ways for generating segments

For water
{first none
last none
auto none }

According to psfgen manual "Because CHARMM uses an additional H-H bond
we must disable generation of angles and dihedrals for segments
containing waters". Does this apply only to TIP3? What about other water

For membranes :
{first none
last none
auto none dihedrals}

This options were used by membrane builder on VMD. Does this also apply
to other lipids like DMPC? Why shouldn't angles be generated in this case?

At last for proteins
{first nter
last cter
auto angles dihedrals}
This options were used by autopsf builder on VMD.

Any help will be very much appreciated.

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