AMBER: MM_PBSA - SASA - Question

From: Deepangi Pandit <dpandit.brandeis.edu>
Date: Tue, 2 Sep 2008 22:10:13 -0400 (EDT)

Hi All:
This is my first time using MM_PBSA so my question may seem basic. I only want to use MM_PBSA to calculate solvent accessible surface area throughout the trajectory. Unfortunately I get error and I do not understand what it means. I tried to refer the manual but still I do not understand all variables.

Can't use an undefined value as an ARRAY reference at /share/apps/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1294.

I checked the line in the file and it states

if(scalar(.{$DATA->[$i]->{$calc}->{$var}}) > 1){
  &calc_moments_of_distr($DATA->[$i]->{$calc}->{$var},
                                      \$ave,\$adev,\$sdev,\$vari,\$skew,\$curt);
   push .{$AVG->[$i]->{$calc}->{$var}}, $ave;
   push .{$STD->[$i]->{$calc}->{$var}}, $sdev;
             }
In my input file I have 3031 atoms all belonging to protein/receptor. 3031 also includes c and n terminal atoms. I am not sure what should be the value of NUMBER_REC_GROUPS, RSTART and RSTOP.

Key input parameters

BOX NO
NTOTAL 3031
NSTART 1
NSTOP 5000
NFREQ 500
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 3031

Thank you.
Deepa
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Received on Wed Sep 03 2008 - 06:07:56 PDT
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