Setting PB to 0 is the way to turn of PB. By large energies what do you
mean? Are you sure you are looking at the Delta table and not the individual
values?
2010/7/9 Catein Catherine <askamber23.hotmail.com>
>
> Dear Sir/Madam,
>
>
>
> I was trying to do a MM-PBSA/GBSA calculation for the tutorial job. Since
> the PBSA cannot be done due to memory problem. I have to turn off the
> setting of PBSA but only allow to do the calculation for GBSA. Here is my
> input file modified from the tutorial input file. However, I found the
> energy calculated are extremely large, so, I am writing to ask if it is the
> proper procedure to turn off PBSA calculation when I am only interested to
> get GBSA binding energy? Did I do anything wrong in the following input
> file? Pls kindly help.
>
>
>
> Thanks a lot.
>
>
>
> =================================================================
> .GENERAL
> PREFIX snapshot
> PATH ./
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> COMPT ./ras-raf.prmtop
> RECPT ./ras.prmtop
> LIGPT ./raf.prmtop
> GC 0
> AS 0
> DC 0
> MM 1
> GB 1
> PB 0
> 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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Received on Fri Jul 09 2010 - 04:00:05 PDT
