AMBER Archive (2000)

Subject: Re: amber problem

From: dek_at_cgl.ucsf.edu
Date: Wed Jan 19 2000 - 11:12:05 CST

Alexandre Gillet writes:
>I have a problem when I am using Xleap to create my topolgy file and
>.crd file.
>When I do a simple minimization ,with sander, of the file obtain with
>Xleap , the Hbond energy is always 0.000 .
>I do not encounter this problem when I built my amber file using PREP
>,EDIT, LINK, PARM.
>I would like to know if someone already face this problem and what is
>the solution to resolve it ?
>I am running the program on SGI irix 4.2.
>I use AMBER 5.

I think the H-BOND energy should be zero with the new force fields (parm95 and
newer). This is because the H-BONDing energy that used to be a 10-12 termi
is now represented by the 1/r electrostatics. Perhaps P/E/L/P is adding
the H-BOND terms to the force field file anyway.

Dave
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Email: dek_at_cgl.ucsf.edu David Konerding WWW: http://picasso.ucsf.edu/~dek
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