Dear Qinghua Liao
Thanks for your reply...
Please elaborate the suggestion you gave.
Where can i find the pbsa.in file?
and where can i get the fill ratio option?
Please let me know the answers
________________________________
From: 廖青华 <fantastic_0919.yahoo.com.cn>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Monday, 18 May, 2009 5:38:47 PM
Subject: 回复： [AMBER] Error running MM _PBSA.pl script
Hi Sir,
What you should do is to add fillratio=3.0 or 4.0 in the file pbsa.in once you get it when running mm_pbsa immediately, the default value of fillratio is 2.0, that's the problem.
Good luck!
Qinghua Liao
________________________________
发件人： Vikas Sharma <vs_vikassharma.yahoo.co.in>
收件人： amber <amber.ambermd.org>
已发送： 2009/5/18(周一), 下午8:00:13
主题： [AMBER] Error running MM _PBSA.pl script
Dear All,
I am using AMBER10... I am using MM PBSA for calculating Binding free energy of a ligand...
i ran 1 ns production MD..
i used the following commands:
mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log and
mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
After i run mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log i get the following error
/opt/amber10/exe/sander -O
-i pbs a_lig.in -o pbsa_lig.8.out -c
/home/bharatam/amberresults1/vikamb_q1results/snap shot_lig.crd.8 -p
/home/bharatam/amberresults1/vikamb_q1/mol.prmtop not successful
mol is the name of my ligand...
How can i overcome this error?????
Please help...
the input files(extract_coords.mmpbsa and binding_energy.mmpbsa) are given below..
extract_coords.mmpbsa:
.GENERAL
PREFIX snapshot
PATH
/home/bharatam/amberresults1/vikamb_q1results
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT
/home/bharatam/amberresults1/vikamb_q1/Awr.prmtop
RECPT
/home/bharatam/amberresults1/vikamb_q1/A.prmtop
LIGPT
/home/bharatam/amberresults1/vikamb_q1/wr.prmtop
#
GC 1
AS 0
DC 0
#
MM 0
GB 0
PB 0
MS 0
#
NM 0
.MAKECRD
BOX YES
NTOTAL 31303
NSTART 1
NSTOP 100
NFREQ 1
#
NUMBER_LIG_GROUPS 1
LSTART 3716
LSTOP 3757
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 3715
.TRAJECTORY
TRAJECTORY /home/bharatam/amberresults1/vikamb_q1/prod1.mdcrd
TRAJECTORY /home/bharatam/amberresults1/vikamb_q1/prod2.mdcrd
binding_energy.mmpbsa
.GENERAL
PREFIX snapshot
PATH
/home/bharatam/amberresults1/vikamb_q1results
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT
/home/bharatam/amberresults1/vikamb_q1/Amol.prmtop
RECPT
/home/bharatam/amberresults1/vikamb_q1/A.prmtop
LIGPT
/home/bharatam/amberresults1/vikamb_q1/mol.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 1
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
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Received on Wed May 20 2009 - 17:20:07 PDT
