Dear all, Im writing because I've been trying to solve a problem with
the mm_pbsa for months but I can not do it. When I calculate the
binding energy for a ligand-enzime complex by mm_pbsa in amber10 using
the following input:
PREFIX tr103-sr25
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT complejo.prmtop
RECPT receptor.prmtop
LIGPT ligando.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 1
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
I received the following problem:
Use of uninitialized value in multiplication (*) at
/home/sergio/Programas/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line
1378.
No data for 0+2 PB PB 0
The output file gave me some warnings:
Reading tr103-sr25_com.all.out
WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
WARNING: Missing EPB for PB in 0 -> Taken from -1
Reading tr103-sr25_rec.all.out
Checking CALC
WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
WARNING: Missing EPB for PB in 0 -> Taken from -1
Reading tr103-sr25_lig.all.out
Checking CALC
WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
WARNING: Missing PB for PB in 0 -> Taken from -1
WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
WARNING: Missing EPB for PB in 0 -> Taken from -1
The energy output for ligand, receptor and complex are:
ligand
MM
GB
PB
MS
1
BOND = 6.4620 ANGLE = 9.0237 DIHED = 15.3520
VDWAALS = -4.9297 EEL = 0.0000 EGB = 0.0000
1-4 VDW = 16.1895 1-4 EEL = 0.0000 RESTRAINT = 0.0000
surface area = 594.734
ECAVITY = 594.734
EDISPER = 0.0000
receptor
MM
GB
PB
MS
1
BOND = 3076.6042 ANGLE = 8300.7106 DIHED = 9726.1992
VDWAALS = -7614.1238 EEL = -73971.1573 EGB = -12444.1021
1-4 VDW = 3708.5404 1-4 EEL = 47222.5091 RESTRAINT = 0.0000
corrected reaction field energy: -20517.454143
surface area = 52994.258
ECAVITY = 52994.258
EDISPER = 0.0000
complex
MM
GB
PB
MS
1
BOND = 3083.0662 ANGLE = 8309.7344 DIHED = 9741.5536
VDWAALS = -7655.2357 EEL = -73971.1573 EGB = -12436.3100
1-4 VDW = 3724.7299 1-4 EEL = 47222.5091 RESTRAINT = 0.0000
corrected reaction field energy: -20505.425856
surface area = 52811.495
ECAVITY = 52811.495
EDISPER = 0.0000
I patched the bugfixes for amber. I've been running mm_pbsa for others
very similar ligands, but I never had this problem before.
I appreciate any kind of help or explanation about this problem.
Thank you very much for your time.
Sergio Ribone.
Dept Pharmacy, Science Chemistry Phaculty
National University of Córdoba
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 15 2011 - 08:30:02 PDT
