The parameters in the input file should be in all capital letters. So
instead of putting "cavity_surften" and "cavity_offset" in the input file
you should be putting "CAVITY_SURFTEN" and "CAVITY_OFFSET." I have tried
this for other input variables and have noticed the the case of the letters
make a difference in the mm_pbsa.pl input file. I hope this helps.
Good luck!
-Bill Miller
2010/3/18 Jeffrey <jeffry20072008.yahoo.cn>
> Dear AMBER users,
> I am going to calculate the binding free energy btw a protein (receptor)
> and a small molecule (ligand) by using the MMPBSA module in AMBER10.
> The input file used for input is as follows:
> ------------------------------------------- mmpbsa-binding.inp
> # Input parameters for mm_pbsa.pl
> .GENERAL
> #
> PREFIX snapshot
> PATH ./
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ./comp.prmtop
> RECPT ./rec.prmtop
> LIGPT ./lig.prmtop
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 1
> PB 1
> MS 0
> #
> NM 0
> #
> ##################################################################
> .DECOMP
> #
> DCTYPE 2
> #
> COMREC 1-304
> COMLIG 305
> COMPRI 1-305
> RECRES 1-304
> RECPRI 1-304
> RECMAP 1-304
> LIGRES 1
> LIGPRI 1
> LIGMAP 305
> #
> .PB
> #
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 2
> LINIT 10000
> PRBRAD 1.4
> ISTRNG 0.0
> RADIOPT 0
> NPOPT 1
> cavity_surften 0.00542
> cavity_offset 0.92
> #
> 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
> ------------------------------
> In this script we set parameters cavity_surften = 0.00542, cavity_offset =
> 0.92 and MS =0.
> Then the nonpolar solvation free energy will be computed by Gnp =
> cavity_surften*SASA + cavity_offset.
> But in the files pbsa_com.in, pbsa_rec.in and pbsa_lig.in, the following
> parameters are found:
> ----
> ...
> &pb
> ...
> cavity_surften = 0.0072, cavity_offset = 0.00,
> npbverb= 1
> &end
> ----
> where cavity_surften = 0.0072 and cavity_offset = 0.00 are used.
> While in the output file mmpbsa-binding.out(mm_pbsa.pl mmpbsa-binding.inp
> > mmpbsa-binding.out),
> the following parameters are found:
> --------
> =>> Values of global variables
> TEMP = 300
> R = 8.314
> gammaP = 1
> betaP = 0
> gammaG = 0.0072
> betaG = 0.000
> ------------------------
> Why the values of cavity_surften and cavity_offset are different in the
> input script (mmpbsa-binding.inp),
> the pbsa_*.in files, and the output file ( mmpbsa-binding.out) ? I am
> really confused...
> Thanks for the time.
>
> Jeffrey Yang
> ---DICP,CAS
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Mar 18 2010 - 08:00:05 PDT
