AMBER Archive (2004)

Subject: Re: AMBER: question about building prmtop and inpcrd files in xleap

From: David A. Case (
Date: Mon Jun 28 2004 - 11:02:37 CDT

On Mon, Jun 28, 2004, wrote:
> Mapped residue ALA, term: Terminal/beginning, seq. number: 0 to: NALA.
> (Residue 1: GLU, Nonterminal, was not found in name map.)

Not to worry about the above. I suppose we should add these to the name
maps in $AMBERHOME/dat/leap/cmd, just to avoid potentially confusing messages.

> Building improper torsion parameters.
> ** Warning: No sp2 improper torsion term for NB-C-CB-CB
> atoms are: N7 C6 C5 C4

Not to worry: see recent mailing list posts on this topic.

> Another question is about water. If I want to include water molecules in
> the crystal structure, what should I do? Do I need to change the name of
> each molecule and add "TER" after that?

Yes, it is best to add TER cards after each separate molecule in your input

...good luck...dac

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to