AMBER Archive (2008)

Subject: Re: AMBER: problems with 10-12 potential in amber8 sander

From: David A. Case (
Date: Thu Feb 28 2008 - 17:47:10 CST

On Thu, Feb 28, 2008, Amie Demmel wrote:

> It seems that we increased the limit in both amber8(at line 81 in rdparm.f the
> check is to 2000) and sander5.0.1 (that check is to 6000). Since our group
> deals with coarse grain models that requires each residue on the protein to be
> considered "unique". Is there a way to safely increase nphb?

Did you also change the sizes of the asol and bsol and hbcut arrays in
parms.h? Note that you also have to change BC_PARMR and BC_PARMI in parms.h
(see the comments) if you are planning to run in parallel.

[It is clear that better code would make all of this stuff dynamic, so
that array bounds were determined at run time. Until then, however, you will
have to take care to make sure you have enough space in these arrays.]

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