AMBER Archive (2008)

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

From: David A. Case (case_at_scripps.edu)
Date: Thu Feb 28 2008 - 16:27:47 CST

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

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