[AMBER] Fwd: MMPBSA problem binding energy calculation

From: kamlesh sahu <kamleshsemail.gmail.com>
Date: Tue, 8 Jun 2010 10:08:07 +0900

Hello amber users,

I am calculating binding energy using these two steps -

$AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log

Then I used following command to calculate binding energy -

$AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log

during the calculation I am getting following warnings --->


odd number of probe positions on torus!
vertex atom mismatch
       atom: 7239
vertex atom: 6871
odd number of probe positions on torus!
odd number of probe positions on torus!
sh: line 1: 21073 Segmentation fault
/home/xtal/amber_10_install/exe/molsurf snapshot_com.pqr.51 0.0
>snapshot_com.mslog.51
odd number of probe positions on torus!
odd number of probe positions on torus!


Could you please tell me what it means. Also I would really appreciate if
you could please tell me if there is any link where I can read about all
such warnings and error messages related to MMPBSA to understand what is
wrong?

Thank you very much
Regards,
kamlesh












---------- Forwarded message ----------
From: kamlesh sahu <kamleshsemail.gmail.com>
Date: Tue, Jun 1, 2010 at 6:42 PM
Subject: MMPBSA problem binding energy calculation
To: amber.ambermd.org


Dear amber users,


Hello
I need your help.



I wish to calculate binding free energy for a complex. So I prepared prmtop
files for the ligand and receptor (pdb contains 3 zinc ions). I also run MD
simulation with the solvated complex structure containing ligand. When I use
mm_pbsa.pl to calculate binding energy it gives following error-



/home/xtal/amber_10_install/exe/sander -O -i sander_com.in -o
sander_com.1.out -c ./snapshot_com.crd.1 -p ./MEK_vac.prmtop not successful






The input files are ---
The extract_coords.mmpbsa file is as follows-


.GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./MEK_vac.prmtop
RECPT ./MEK_minus_SAM_vac.prmtop
LIGPT ./SAM_vac.prmtop
GC 1
AS 0
DC 0
MM 0
GB 0
PB 0
MS 0
NM 0
.MAKECRD
BOX YES
NTOTAL 3560
NSTART 1
NSTOP 200
NFREQ 1
NUMBER_LIG_GROUPS 1
LSTART 3359
LSTOP 3385
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 3355
.TRAJECTORY
TRAJECTORY ./md1.mdcrd
TRAJECTORY ./md2.mdcrd
.PROGRAMS

I TRIED WITH SOME MODIFICATIONS OF THIS FILE ALSO.... LIKE IF I INCLUDE Zn
IONS, RSTOP=3358,... but again the same error.

The binding_energy.mmpbsa file -

.GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./MEK_vac.prmtop
RECPT ./MEK_minus_SAM_vac.prmtop
LIGPT ./SAM_vac.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

First I extracted the snapshots using command -

$AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log

Then I used following command to calculate binding energy -

$AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log

I got this error --->

/home/xtal/amber_10_install/exe/sander -O -i sander_com.in -o
sander_com.1.out -c ./snapshot_com.crd.1 -p ./MEK_vac.prmtop not successful



Kindly suggest me the ways to improve my calculation.



Thank you

Regards,

kamlesh
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 07 2010 - 18:30:03 PDT
Custom Search