Dear all,
I'm trying to use MM_PBSA to calculate a protein-ligand binding energy,but unluckily,I received a message like this:
Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
No data for 0+0 NM SROT 0
For details see: http://ambermd.org/Questions/mm_pbsa.html#calc_delta_no_data_plus_zero
It has produced the output files:snapshot_com.all.out,snapshot_rec.all.out,snapshot_lig.all.out,but not "snapshot_statistics.out " file.I don't know how to work it out .My input file is like this :
.GENERAL
PREFIX snapshot
PATH ./snapshot
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./comp_ini.prmtop
RECPT ./protein.prmtop
LIGPT ./ind.prmtop
GC 0
AS 0
DC 0
MM 1
GB 1
PB 1
MS 1
NM 1
.PB
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
.MM
DIELC 1.0
.GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00
.MS
PROBE 0.0
.NM
PROC 2
DIELC 4
MAXCYC 10000
DRMS 0.1
IGB 0
.PROGRAMS
Many thanks !
jinfengliu
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Received on Fri Jul 22 2011 - 02:00:03 PDT
