Dear amber users,
I have several questions about mmpbsa(I am using amber 7 under redhat
linux 9.0):
1. when I run mm_pbsa.pl, I always get the error message on the screen
as following:
Illegal character in prototype for mm_pbsa_statistics::mm_pbsa_stat :
$calc_delta,$calc_dec,$input,$output,$snap_min,$snap_max at
/usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 275.
....
....
Illegal character in prototype for main::final_clean_up : \%GEN,\%DEL at
/usr/local/amber7/exe/mm_pbsa.pl line 1644.
but looks like the script keeps running and outputs the final results to
xxx_statistics.out(job is "Done", not "Exit"). Does anybody know what
these error messages mean? Do they affect the results?
2. In the output file, mmpbsa.out, I always find some warnings:
Reading d3hvpMD_com.all.out
WARNING: Missing GB for GB in 21 -> Taken from 20
WARNING: Missing SURF for MS in 34 -> Taken from 33
WARNING: Missing SURF for MS in 58 -> Taken from 57
Reading d3hvpMD_rec.all.out
Checking CALC
WARNING: Missing SURF for MS in 58 -> Taken from 57
Reading d3hvpMD_lig.all.out
Checking CALC
WARNING: Missing SURF for MS in 58 -> Taken from 57
WARNING: Missing SURF for MS in 62 -> Taken from 61
WARNING: Missing SURF for MS in 70 -> Taken from 69
is it normal or something wrong?
3. Today, one of my jobs is "Exit 25", not "Done". I checked the output
file, and found the job was stop at "Calc Delta" :
Processing GB GBTOT
Doing 1 GB GBSOL
Doing 1 MM GAS
Doing 1 GB GBSOL
Doing 1 MM GAS
Doing 1 GB GBSOL
Doing 1 MM GAS
=>> Calc delta
Does anybody know what's the problem here?
Thank you so much
All the best
Shawn Hu
Chem. Depart.
Univ. of Memphis
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Mar 03 2004 - 19:53:01 PST
