AMBER Archive (2009)

Subject: 回复： [AMBER] Error running MM _PBSA.pl script

From: 廖青华 (fantastic_0919_at_yahoo.com.cn)
Date: Mon May 18 2009 - 07:08:47 CDT

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_at_yahoo.co.in>
收件人： amber <amber_at_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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