Hi,
I don't think you can get what you want with the 'molsurf' command.
What it does is calculate the Connolly surface area of atoms specified
by <mask>, *not* the contribution of the atoms in <mask> to the
overall surface area. So the surface area of a single amino acid is
going to be pretty similar between different systems.
You could try using the 'surf' command instead, which does actually
calculate the contribution of atoms in <mask> to the overall surface
area. It uses the less accurate LCPO algorithm, but for the sake of
comparing different systems it's probably OK as long as no large-scale
conformational changes are occurring.
-Dan
On Wed, Mar 2, 2016 at 2:58 PM, George Tzotzos <gtzotzos.me.com> wrote:
> I’ve been trying to work out the effect of ligand binding on homodimer formation. I’m dealing with 2 X-ray structures involving the same receptor bound to two different ligands.
>
> The ligands bind on the homodimer interface (one per subunit). The subunit main cavity is occupied by serendipitous ligands.
>
> I performed explicit solvent MD simulations of the dimer complexes in which the serendipitous ligands were stripped. The starting coordinates and conformations of the biological ligands were as per X-ray model. I also performed two separate MD simulations (a) dimer without any ligands (serendipitous or biological) and (b) monomer without any ligands.
>
> I used cpptraj molsurf to obtain the SASAs of the dimer interface residues. A typical example of a cpptraj input is:
>
> parm complex_solv.prmtop
> trajin prod_0-100ns.nc 1 10000 200
> molsurf IntRes :71 out Val71.dat
>
> The process was repeated for each interface residue for (1) monomer stripped of ligands; (2) dimer stripped of ligands; (3) dimer with ligand_1; (4) dimer with ligand_2
>
> The dimer interface consists of 28 residues.
>
> For all residues I obtained the same SASA. Typical examples are shown below.
>
>
> Val71
> His72
> Leu73
> Glu74
> His77
> monomer_apo
> 129.926556
> 154.186386
> 148.421838
> 142.796564
> 154.709454
> dimer_apo
> 129.384386
> 154.215862
> 148.084478
> 143.101678
> 153.807794
> dimer_deet
> 130.021954
> 154.398068
> 149.21626
> 143.135464
> 154.704514
> dimer_6MH
> 129.644992
> 154.301966
> 149.275882
> 143.195312
> 154.090458
>
> I find these results hard to explain unless the above input script is wrong.
>
> Any suggestions would be most welcome
>
> Regards
>
> George
>
>
>
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Mar 03 2016 - 08:00:03 PST
