AMBER Archive (2004)

Subject: AMBER: questions about mmpbsa

From: xhu1_at_memphis.edu
Date: Wed Mar 03 2004 - 13:48:12 CST

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

                                                     

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