Also, I have a followed-up question. No matter what cavity_surften and
cavity_offset settings I used in MM/PBSA, as long as other settings are the
same, is the SASA term calculated by same program PBSA? Since I chose inp=1
which is a linear model, theoretically the average Enp could be transformed
directly without recalculating MM/PBSA if I only want to get different
Enp...Is that correct?
Thanks!
Guqin
On Tue, Aug 29, 2017 at 2:35 PM, Guqin Shi <shi.293.osu.edu> wrote:
> Dear all,
>
> I have a simple question that I hope somebody could clarify for me. It's
> about the Gnp settings in MM/PBSA.
>
> &pb and &gb has different namelist variables. I am using inp=1 option
> which calculates Gnp linearly to SASA (gamma*SASA+b). There are different
> sets of gamma and b.
>
> In &pb namelist, I used cavity_surften (gamma) and cavity_offset (b) to
> change the settings for Gnp.
> (In &gb namelist, surften (gamma) and surfoff (b) are used.)
>
> I usually ask program to print out all temporary files for me during
> MM/PBSA. There is one file _MMPBSA_info which contains all input
> parameters. I checked this file and noticed that both surften, surfoff,
> cavity_surften, and cavity_offset are listed. surften and surfoff are their
> default values (according to Amber manuals under &gb section). I am a
> little bit confused. So here _MMPBSA_info file just listed all parameters
> but eventually if I specified &pb, then the program will only use
> cavity_surften and cavity_offset for Gnp calculation, right? I want to make
> sure I pass the correct parameters to the program...
>
> Thank you a lot!
> -Guqin
>
> --
> Guqin SHI
> PhD Candidate in Medicinal Chemistry and Pharmacognosy
> College of Pharmacy
> The Ohio State University
> Columbus, OH, 43210
>
>
--
Guqin SHI
PhD Candidate in Medicinal Chemistry and Pharmacognosy
College of Pharmacy
The Ohio State University
Columbus, OH, 43210
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Received on Tue Aug 29 2017 - 13:30:03 PDT
