AMBER Archive (2007)

Subject: AMBER: Missing values for MM ELE (MM-PBSA)..help!!

From: Rima Chaudhuri (rima.chaudhuri_at_gmail.com)
Date: Wed Feb 07 2007 - 10:21:38 CST

Hi All,
A brief about my inputs:
The trajectory from the simulation of the protein-ligand-complex in a water
box, was stripped off water and counterions. This stripped trajectory and
the unsolvated prmtop files of the protein, ligand (small organic
molecule) and complex were used to generate 100 snapshots. When I try to run
the binding energy calculations using these snapshots, it gives me the
following message consistently: (I am not using Delphi)

Use of uninitialized value in concatenation (.) or string at
/hprog/amber8/src/mm_pbsa/mm_pbsa_readinput.pm line 76, <IN> line 57.
Use of uninitialized value in exists at
/hprog/amber8/src/mm_pbsa/mm_pbsa_readinput.pm line 80, <IN> line 57.
Use of uninitialized value in hash element at
/hprog/amber8/src/mm_pbsa/mm_pbsa_readinput.pm line 84, <IN> line 57.
Use of uninitialized value in hash element at
/hprog/amber8/src/mm_pbsa/mm_pbsa_readinput.pm line 84, <IN> line 57.

                *Missing values for MM ELE
*
The log file is as follows: I am sure that the mdcrd file is stripped off
water and ions and the prmtop files are unsolvated. On cross-checking with
the example files in the src/mm_pbsa/Examples folder, it found that the
output in my case looks different after ' Calculating energy /entropy ...'
seems like the program is not doing any calculations at all with my
input/snapshots. What am I doing wrong.

=>> Reading input parameters
    Found PREFIX => 1nfu_binding
    Found PATH => snapshots/
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT => 1nfu_lig_complex.prmtop
    Found RECPT => 1nfu_ca_only.prmtop
    Found LIGPT => 1nfu_lig.prmtop
    Found =>
    Found GC => 0
    Found AS => 0
    Found DC => 0
    Found MM => 1
    Found GB => 1
    Found PB => 1
    Found MS => 1
    Found NM => 1
    Found PROC => 2
    Found REFE => 0
    Found INDI => 1.0
    Found EXDI => 80.0
    Found SCALE => 2.0
    Found LINIT => 1000
    Found PRBRAD => 1.4
    Found RADIOPT => 0
    Found SURFTEN => 0.00542
    Found SURFOFF => 0.92
    Found DIELC => 1.0
    Found IGB => 2
    Found GBSA => 1
    Found SALTCON => 0.00
    Found EXTDIEL => 80.0
    Found INTDIEL => 1.0
    Found SURFTEN => 0.0072
    Found SURFOFF => 0.00
    Found PROBE => 0.0
    Found DIELC => 4
    Found MAXCYC => 1000
    Found DRMS => 0.1
=>> Checking sanity
    Checking GENERAL
    Checking MM
    Checking NM
    Checking PB
    Checking GB
    Checking MS

=>> Creating input
    Sander input
    PBSA input
    Nmode input

=>> Calculating energy / entropy contributions

=>> Doing statistics
=>> Values of global variables
    TEMP = 300
    R = 8.314
    gammaP = 0.00542
    betaP = 0.92
    gammaG = 0.0072
    betaG = 0.00
=>> Reading input
=>> Reordering files
    Final order:
    1. 1nfu_binding_com.all.out: -
     2. 1nfu_binding_rec.all.out: -
    3. 1nfu_binding_lig.all.out: -
=>> Reading files
    Reading 1nfu_binding_com.all.out
    Reading 1nfu_binding_rec.all.out
    Reading 1nfu_binding_lig.all.out
=>> Treat special parameters
=>> Calc missing parameters
    Processing MM ELE
    Processing MM GAS
    Processing MM INT
    Processing MM VDW
    Processing GB GBTOT
    Processing GB GBELE
    Processing GB GBSOL
    Processing PB PBSOL
    Processing PB PBELE
    Processing PB PBTOT
=>> Calc delta from raw data

Any help will be much appreciated.

Thanks

Rima

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu