AMBER: MM-PBSA: decompose energy error

From: jitrayut jitonnom <jitrayut.018.gmail.com>
Date: Mon, 23 Apr 2007 18:31:43 +0700

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

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Received on Wed Apr 25 2007 - 06:07:18 PDT
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