AMBER Archive (2004)

Subject: Re: AMBER: Star like (branching) molecule

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Feb 24 2004 - 17:51:10 CST

More accurately on my last post:

> > Yesterday I had asked how to build a star like molecule if only 1 tail
> > can be defined.
>
> The head, tail and connect atoms are for automated bonding,
> i.e. on reading in a pdb file.

Or when using leap's 'sequence' command, I forgot to mention.
Using 'sequence' with head and tail defined is indeed one way
to build a structure (which may or may not have steric
problems, since leap makes no effort to avoid them).

> You can bond any atoms with the 'bond' command, ignoring the
> head/tail/connect attributes of the atoms.

This would be appropriate if one had a pdb of the structure, with
TER cards between the parts to be joined.

Bill

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