Dear amber users
I am doing MM-PBSA calculation for my protein-ligand system based on TUTORIAL
A3: MM-PBSA <http://ambermd.org/tutorials/advanced/tutorial3/index.htm>
using AmberTools 14.
I encountered a problem in section 3 of this tutorial:
http://ambermd.org/tutorials/advanced/tutorial3/section3.htm
After successfully extracting of snapshots, I prepared input file (
binding_energy.mmpbsa).
--------------------------------------------------------------------------------------------------
.GENERAL
VERBOSE 0
PARALLEL 0
PREFIX snapshot
PATH ./
START 200
STOP 300
OFFSET 1
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./comp1.prmtop
RECPT ./hsa1.prmtop
LIGPT ./sal1_h.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 5
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
NPOPT 1
ARCRES 0.0625
INP 1
SURFTEN 0.005
SURFOFF 0.00
IVCAP 0
CUTCAP -1.0
XCAP 0.0
YCAP 0.0
ZCAP 0.0
.MM
DIELC 1.0
.GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.005
SURFOFF 0.00
.MS
PROBE 0.0
.NM
DIELC 4
MAXCYC 1000
DRMS 0.1
.PROGRAMS
--------------------------------------------------------------------------------------------------
Then I used this command:
$AMBERHOME/bin/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
But I get following:
Param PROC does not exist
For details see:
http://ambermd.org/Questions/mm_pbsa.html#testpar_param_not_existent
How to resolve this problem?
Any help will highly appreciated.
Best wishes,
Atila
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 04 2015 - 00:00:03 PST
