RE: AMBER: Problem with sander tutorial.

From: tarek mahfouz <>
Date: Thu, 22 Jul 2004 09:59:42 -0700 (PDT)

Hi Ross,
Thanks for our response. I think we have a problem with the amber7 installed on our unix system.
We compiled amber7 on a linux machine yesterday (gentoo linux) using intel fortran compiler version 8 and we were trying to run the tests. Except for different results for energy values from what you got, it run ok.
However, we had the following problem with the ubiquitin and dhfr tests. The error message said "non bond list overflow". We decreased the cut off value (from 9 to 8) but still the problem exists. Here is what the message said:
 using 5000.0 points per unit in tabled values
 TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
 * NB pairs 916 8243196 exceeds capacity ( 8243681) 0
     SIZE OF NONBOND LIST = 8243681
 EWALD BOMB in subroutine ewald_list
 Non bond list overflow!
 check MAXPR in locmem.f

We noticed that the capacity changes as the size of non bond list changes so we always get this error.
So, what would be the parameter to change here?

Ross Walker <> wrote:
Dear Tarek,
There is no format change for the prmtop file between amber 7 and amber 8. However, there was a change between amber 6 and amber 7. Are you certain you are using amber 7?
Also, do you know if you amber 7 installation passes all the tests? Can you run other simulations with it?
Did you create the prmtop file yourself following the tutorial instructions or did you just download the one that is linked to on the website. Have you tried both? Do you get the same error message in each case?
A couple of things to try. First of all see if you can read the prmtop file with rdparm:
rdparm polyAT_vac.prmtop
look out for any error messages as it loads.
Secondly you could try converting it to an old format prmtop file:
new2oldparm < polyAT_vac.prmtop > polyAT_vac.prmtop.old
I have tested the whole tutorial with Amber7 and it all works so there must be something wrong with your installation or the way your machine has downloaded the prmtop file. Are you on a unix machine or a windows machine?
If you can attach the prmtop file you are using to the email it would be great.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

From: [] On Behalf Of tarek mahfouz
Sent: 20 July 2004 12:10
Subject: AMBER: Problem with sander tutorial.

I'm trying to run the DNA polyAT tutrial (amber 8) and I have amber 7 on irix
but sander is not runing the minimization in. First I got an error message about the input file, I changed the last line in the input file to end with &end statement instead of the /
Still sander is not runing but this time the error is different. This time the message said:
fmt: read unexpected character
apparent state: unit 8 named polyAT_vac.prmtop
last format: (12I6)
Unit 8 is a sequential formatted external file
*** Execution Terminated (115) ***

I do not now if there is format change between amber 7 and 8 in the prmtop file format and so I'm not able to solve the problem.
I'm a new user of amber so please any help will be appreciated.

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Received on Thu Jul 22 2004 - 18:53:00 PDT
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