What was in the sander_com1.out?
T. Dwight McGee Jr.
On Jun 1, 2010, at 5:42 AM, kamlesh sahu <kamleshsemail.gmail.com>
wrote:
> 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 ---à
> 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
>
>
> --
> Kamlesh Kumar Sahu
> wako-shi (saitama)
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Received on Tue Jun 01 2010 - 07:30:05 PDT
