AMBER Archive (2004)

Subject: AMBER: pls forget my first question in my last email

From: xhu1_at_memphis.edu
Date: Wed Mar 03 2004 - 14:02:06 CST

Sorry about that! --shawn

----- Original Message -----
From: <xhu1_at_memphis.edu>
Date: Wednesday, March 3, 2004 1:48 pm
Subject: AMBER: questions about mmpbsa

> 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/loca...
> ...
> Illegal character in prototype for main::final_clean_up :
> \%GEN,\%DEL at
> /usr/loca
> 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
> outputfile, 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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