Thank you Dan,
I think that 'molsurf' is not implemented by cpptraj. I assume that in order to use 'molsurf' I shall have to build up the molecules using NAB. Am I right in this?
Regards
George
On Aug 24, 2012, at 4:37 PM, Daniel Roe wrote:
> Hi,
>
> On Fri, Aug 24, 2012 at 7:22 AM, George Tzotzos <gtzotzos.me.com> wrote:
>> In terms of the ligand, the above matches what has been reported in the literature (ligand effectively buried). I have difficulties interpreting the situation with the protein. I would expect that the proteins SASA during the time evolution of the trajectory would be less than that of the apoprotein.
>
> To me, it doesn't seem unreasonable that the SASA of the complexed
> protein is greater than that of the protein by itself. It could be
> that there are some subtle conformational changes that occur in the
> protein upon binding that result in it having a larger SASA overall.
>
> One thing you could try would be to calculate the surface area with
> the 'molsurf' command instead, which gives the more accurate Connolly
> surface area ('surf' uses the LCPO algorithm) and see if the trend
> still holds.
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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Received on Fri Aug 24 2012 - 08:30:03 PDT
