AMBER Archive (2008)

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

From: Amie Demmel (
Date: Thu Feb 28 2008 - 16:53:15 CST

Quoting "David A. Case" <>:

> On Thu, Feb 28, 2008, Amie Demmel wrote:
> >
> >
> > In order to get sander to read my prmtop file (I am using an oldstyle
> > prmtop) I had to modify rdparm.f file and "reset" nphb and nptra
> > variables. Both of these varibles were fine until rdparm read in
> > absol values and then nphb = 1106298783(orig. nphb = 1653) and
> > nptra = 536870912(orig. nptra = 108), these changes in value caused
> > problems in reading in the rest of the prmtop.
> This is weird. At about line 81 of rdparm.f (in Amber 8), there is a
> check that nphb must be less than 200, otherwise the program stops with an
> error message. The first thing is to try to figure out why this statment
> is not being triggered.
> When the program continues, it reads data into asol and bsol outside of their
> array bounds, and after that you are hosed. There is no point in "resetting"
> the values of nphb or nptra: the entire parm data structure will have been
> corrupted at this point.
> Sander5.0.1 has the same error check, however, so I'm puzzled as to why
> things
> seem to work there. The limit of 200 on the variable nphb has been in the
> code for decades -- how did you construct the prmtop file, such that it
> violates this limit?
> ...dac
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?


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