AMBER Archive (2007)

Subject: AMBER: Amber9 Sander Error

From: A Box (boxtwin2_at_gmail.com)
Date: Thu Mar 29 2007 - 20:26:21 CST

Dear Amber Users

When I used Sander in Amber9 I got the following error messege from the
Amber-Test.e****** file. The error

1525-097 A READ statement using decimal base input found the invalid digit
'&' in the input file. The program will recover by assuming a zero in its
place.
1525-097 A READ statement using decimal base input found the invalid digit
'e' in the input file. The program will recover by assuming a zero in its
place.
1525-097 A READ statement using decimal base input found the invalid digit
'n' in the input file. The program will recover by assuming a zero in its
place.
1525-097 A READ statement using decimal base input found the invalid digit
'd' in the input file. The program will recover by assuming a zero in its
place.
1525-097 A READ statement using decimal base input found the invalid digit
'#' in the input file. The program will recover by assuming a zero in its
place.
1525-097 A READ statement using decimal base input found the invalid digit
'#' in the input file. The program will recover by assuming a zero in its
place.
1525-088 The NAMELIST READ statement cannot be completed because item ADE is
not a member of the NAMELIST group rst. The program will recover by
discontinuing further processing of the READ statement.

which was repeated for 9837 lines followed by

1525-090 The NAMELIST READ statement cannot be completed because an
incorrect character was encountered in a NAMELIST group name or item name.
The program will recover by discontinuing further processing of the READ
statement.
1525-090 The NAMELIST READ statement cannot be completed because an
incorrect character was encountered in a NAMELIST group name or item name.
The program will recover by discontinuing further processing of the READ
statement.

which was then repeated for 104 lines

With this I also got a md.out file that had no information in it (an empty
file). When I did the run in Amber8, Sander printed out an error for the
restraint file I had read in and I was then able to fix the file and get it
to run with Sander in Amber9. ut if I did not have Amber8, I would not have
been able to sort out the probelm with the run (I had tried removing the
restraint file, and had dicsoved that to be the source of the error, but I
still had no idea as to why it failed).

So, I ask the question: Why does Amber8 read out the erro for an incorrect
restraint file (R3 value was greater than R2), yet Amber9 does not?

Thanks in advance.

Andrew Box.

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