Jason,
Thanks for your comments. I am trying to compare GBSA calculations through
mm_pbsa.pl using Amber 8 and Amber10. I have used the same amber8 input
script to perform GBSA calculations using amber10. The script is
generating all the files expect snapshot_statistics.out. I am getting the
following in the .log file
Calc contrib for ./snapshot_lig.crd.25
Calc MM/GB/SAS
Generate PDB
Center PDB
Generate PQR
Calc MS
=>> 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: -
2. snapshot_rec.all.out: -
3. snapshot_lig.all.out: -
=>> Reading files
Reading snapshot_com.all.out
WARNING: Missing SROT for NM in 0 -> Taken from -1
WARNING: Missing STOT for NM in 0 -> Taken from -1
WARNING: Missing STRA for NM in 0 -> Taken from -1
WARNING: Missing SVIB for NM in 0 -> Taken from -1
WARNING: Missing SROT for NM in 1 -> Taken from 0
WARNING: Missing STOT for NM in 1 -> Taken from 0
WARNING: Missing STRA for NM in 1 -> Taken from 0
WARNING: Missing SVIB for NM in 1 -> Taken from 0
WARNING: Missing SROT for NM in 2 -> Taken from 1
WARNING: Missing STOT for NM in 2 -> Taken from 1
WARNING: Missing STRA for NM in 2 -> Taken from 1
WARNING: Missing SVIB for NM in 2 -> Taken from 1
WARNING: Missing SROT for NM in 3 -> Taken from 2
WARNING: Missing STOT for NM in 3 -> Taken from 2
WARNING: Missing STRA for NM in 3 -> Taken from 2
WARNING: Missing SVIB for NM in 3 -> Taken from 2
WARNING: Missing SROT for NM in 4 -> Taken from 3
WARNING: Missing STOT for NM in 4 -> Taken from 3
WARNING: Missing STRA for NM in 4 -> Taken from 3
WARNING: Missing STRA for NM in 98 -> Taken from 97
WARNING: Missing SVIB for NM in 98 -> Taken from 97
WARNING: Missing SROT for NM in 99 -> Taken from 98
WARNING: Missing STOT for NM in 99 -> Taken from 98
WARNING: Missing STRA for NM in 99 -> Taken from 98
WARNING: Missing SVIB for NM in 99 -> Taken from 98
WARNING: Missing SROT for NM in 100 -> Taken from 99
WARNING: Missing STOT for NM in 100 -> Taken from 99
WARNING: Missing STRA for NM in 100 -> Taken from 99
WARNING: Missing SVIB for NM in 100 -> Taken from 99
WARNING: Missing SROT for NM in 101 -> Taken from 100
WARNING: Missing STOT for NM in 101 -> Taken from 100
WARNING: Missing STRA for NM in 101 -> Taken from 100
WARNING: Missing SVIB for NM in 101 -> Taken from 100
Reading snapshot_rec.all.out
Checking CALC
and also
Talon-login[115] mhb75$ less test11.e120494
Calc mode NM not found
Permission denied.
This is my input file:
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./hAChE.prmtop
RECPT ./hAChE-sarin.prmtop
LIGPT ./MMB.prmtop
GC 0
AS 0
DC 0
MM 1
GB 1
PB 0
MS 1
NM 0
.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
.PROGRAMS
I have made NM==0, and I don't understand why it is complaining about NM?
Any suggestions?
mani
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jul 17 2011 - 22:30:03 PDT
