AMBER Archive (2004)

Subject: AMBER: MMPBSA problem

From: John (john.dalmaris_at_imperial.ac.uk)
Date: Thu Jun 03 2004 - 11:09:05 CDT

Hello Amber users,

I was wondering if anyone has any suggestions on the following problem. I am
trying to run the MMPBSA examples on Amber7 but only the "GenerateSnapshot"
runs until the end. The rest terminate soon after and the last entry in the
log file is:

>> Reading files
    Reading ras_raf_II_wt_com.all.out
    Reading ras_raf_II_wt_rec.all.out
    Reading ras_raf_II_wt_lig.all.out
=>> Treat special parameters

Also here are some lines of the error messeges I get:

Illegal character in prototype for main::calc_PB :
$OUT,$pdbbase,$outbase,\%DEL,\%PRO at /usr/local/amber7/exe/mm_pbsa.pl line
1512.
Illegal character in prototype for main::calc_statistics :
\%GEN,\%DEC,\%DEL,\%GBO,\%PRO at /usr/local/amber7/exe/mm_pbsa.pl line 1566.
Illegal character in prototype for main::final_clean_up : \%GEN,\%DEL at
/usr/local/amber7/exe/mm_pbsa.pl line 1644.
Can't use an undefined value as an ARRAY reference at
/usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1234.

As suggested in a similar problem I have already comment the line "unlink
$sanout;" in "sub calc_MM_GB_SAS" in mm_pbsa.pl but I get the same result.

I use Amber7 in Red Hat 9 and installed the executable for Delphi 2.0.

Thank you in advance for your help.

Best wishes,

John

 

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