AMBER Archive (2007)

Subject: AMBER: MM-PBSA: decompose energy error

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Mon Apr 23 2007 - 06:31:43 CDT

Dear amber users,

I have problem on running mmpbsa using AMBER9 to obtain the decompose
energy. After i extracted 100 snapshots and then performed the
decompose_energy.in as show below; i found the error during the mmpbsa
process like this

" Missing values for MM BGAS "

When i check the end of the log file of this process, it stop at line below;

=>> 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. snapshot_com.all.out: 1 - 237
    2. snapshot_rec.all.out: 1 - 230
    3. snapshot_lig.all.out: 231 - 237
=>> Reading files
    Reading snapshot_com.all.out
    Reading snapshot_rec.all.out
    Checking CALC
    Reading snapshot_lig.all.out

For the decompose_energy.in are following;

@GENERAL
PREFIX snapshot
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./enz-lig.top
RECPT ./enz.top
LIGPT ./lig.top
#
GC 0
AS 0
DC 1
#
MM 1
GB 1
PB 0
MS 0
#
NM 0
############################################################################

@DECOMP
DCTYPE 2
#
COMREC 1-230
COMLIG 231-237
COMPRI 1-237
RECRES 1-230
RECPRI 1-230
RECMAP 1-230
LIGRES 231-237
LIGPRI 231-237
LIGMAP 231-237
############################################################################
@MM
DIELC 1.0
############################################################################
@GB
IGB 2
GBSA 2
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00

So, any suggestions will be grate.

Thank you in advance,

Jitrayut Jitonnom

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