On Wed, Dec 25, 2013 at 4:35 AM, Yanyan ZHU <zhuyanzily.gmail.com> wrote:
> Dear amber:
>
> The MMPBSA.pl was used to calculate the decomposing binding energy and the
> input file was as following:
>
> ##################################################
>
> .GENERAL
>
> VERBOSE 0
>
> PARALLEL 0
>
> #
>
> PREFIX wat
>
> PATH ./
>
> START 1
>
> STOP 100
>
> OFFSET 1
>
> #
>
> COMPLEX 1
>
> RECEPTOR 1
>
> LIGAND 1
>
> #
>
> COMPT ./x-wat-com.prmtop
>
> RECPT ./x-wat-pro.prmtop
>
> LIGPT ./x-wat-lig.prmtop
>
> #
>
> GC 0
>
> AS 0
>
> DC 1
>
> #
>
> MM 1
>
> GB 0
>
> PB 1
>
> MS 0
>
> #
>
> NM 0
>
> #
>
> .DECOMP
>
> #
>
> DCTYPE 2
>
> #
>
> COMREC 1-276
>
> COMLIG 277-277
>
> COMPRI 1-276 277-277
>
> RECRES 1-276
>
> RECPRI 1-276
>
> RECMAP 1-276
>
> LIGRES 1-1
>
> LIGPRI 1-1
>
> LIGMAP 277-277
>
> #
>
> .PB
>
> PROC 2
>
> REFE 0
>
> INDI 1.0
>
> EXDI 56.97
>
> SCALE 2
>
> LINIT 1000
>
> PRBRAD 1.4
>
> ISTRNG 0.0
>
> RADIOPT 1
>
> INP 0
>
> #
>
> SURFTEN 0.04356
>
> SURFOFF -1.008
>
> #
>
> IVCAP 0
>
> CUTCAP -1.0
>
> XCAP 0.0
>
> YCAP 0.0
>
> ZCAP 0.0
>
> #
>
> .MM
>
> DIELC 1.0
>
> #
>
> .GB
>
> IGB 2
>
> GBSA 2
>
> SALTCON 0.00
>
> EXTDIEL 56.97
>
> INTDIEL 1.0
>
> #
>
> SURFTEN 0.0072
>
> SURFOFF 0.00
>
> #
>
> .MS
>
> PROBE 0.0
>
> #
>
> ##############################################################
>
> However, the file of statistics.out was not obtained in the end. And
> then when we opened the files of com.all.out, rec.all.out, lig.all.out, all
> of the values for PBSUR (the last column) were zero.
I don't think the surface area term is decomposable in PB. Also, I don't
think the Perl script prints out the statistics.out file when you are doing
decomposition (MMPBSA.py does, though).
>
> Can you give me a hand
>
> about this problem?
Try MMPBSA.py instead, since that script tends to receive more support on
this list.
Good luck,
Jason
P.S.
GB energies are more easily decomposed than PB energies. Since neither GB
or PB energies are really decomposable, anyway, decomposition energies have
only limited use in certain comparisons between related systems.
Therefore, using PB does not really offer a more 'reliable' decomposed
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Dec 25 2013 - 07:00:02 PST
