AMBER Archive (2008)

Subject: AMBER: MM_PBSA problems in AMBER9

From: 欧阳德方 (ouyangdf1978_at_hotmail.com)
Date: Sun Oct 05 2008 - 16:30:12 CDT

Hi, all,

When I calculate the binding energy of RNA-small molecule interaction by MM_PBSA in AMBER9. Input file is as following:

PREFIX snapshot
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./den4_complex_major_vac.prmtop
RECPT ./rna_vac.prmtop
LIGPT ./dendrimer4.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 1
MS 1
#
NM 0
#
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
NPOPT 1
CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00
#
SURFTEN 0.0072
SURFOFF 0.00
#
DIELC 1.0
#
#
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
#
PROBE 0.0
#

But it shows "---snapshot_lig.crd.17 not successful---"
The output file shows
"---PB Bomb in setgrd (): focusing grid too large 2
reset fillratio to a large number 2.000"

According previous post, I change SCALE 2.0 to 4.0 (or 3.0). But new problems appears.
The output file shows:
"---
    WARNING: Missing PB for PB in 0 -> Taken from -1
    WARNING: Missing PB for PB in 1 -> Taken from 0
    WARNING: Missing PB for PB in 2 -> Taken from 1 

---
=>> Calc delta from raw data"

Also the command lines shows:
" ---
Use of uninitialized value in multiplication (*) at /usr/local/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
Use of uninitialized value in multiplication (*) at /usr/local/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
    No data for 0+2 PB PB 0"

I cannot get the final statistical output file.

Could u tell me the reasons and how to solve it?

Thanks for your help,

Ouyang 

School of Pharmacy
The University of Queensland
Brisbane, Australia 

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