AMBER Archive (2008)

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

From: Lynn F. Ten Eyck (
Date: Thu Feb 28 2008 - 16:54:47 CST

These values look suspiciously as though nphb and nptra are getting
hit with floating point numbers. If you have changed the read
routine, make sure you haven't read data with the wrong format, or
overrun an array index on input.

Lynn Ten Eyck

On 28 Feb 2008, at 14:27, David A. Case wrote:

> 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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Lynn F. Ten Eyck Office: 3131 Atkinson Hal
UCSD /MC 0505 Tel: +858.534.5141
San Diego Supercomputer Center Fax: +858.822.3610
9500 Gilman Drive
La Jolla, CA 92093-0444

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