AMBER Archive (2009)

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

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Mon May 18 2009 - 09:06:49 CDT

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_at_yahoo.com.cn>
To: AMBER Mailing List <amber_at_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_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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