AMBER Archive (2004)

Subject: RE: AMBER: Problem with sander tutorial.

From: Ross Walker (
Date: Tue Jul 20 2004 - 15:16:28 CDT

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
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
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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