AMBER Archive (2004)

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

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

On Mon, Jun 28, 2004, jz7_at_duke.edu 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
file.

...good luck...dac

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