AMBER Archive (2009)

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

From: 廖青华 (fantastic_0919_at_yahoo.com.cn)
Date: Mon May 18 2009 - 09:41:14 CDT

Hi Sir,

The file of pbsa.in is generated once you run mm_pbsa, which is located in your working fold. You can open the file pbsa.in, and then add a line "fillratio=4.0" in the file. Save it, and it will be ok!

Good luck!

Qinghua Liao

________________________________
发件人： Vikas Sharma <vs_vikassharma_at_yahoo.co.in>
收件人： AMBER Mailing List <amber_at_ambermd.org>
已发送： 2009/5/18(周一), 下午10:06:49
主题： Re: 回复： [AMBER] Error running MM _PBSA.pl script

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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