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
