[AMBER] Molsurf: some questions on usage

From: George Tzotzos <gtzotzos.me.com>
Date: Thu, 27 Aug 2015 18:05:44 +0300

I’m trying to calculate the Connolly SASA of a ligand in the free and bound state.

I’m using the following input script for the complex.trj

parm complex_solv.prmtop
trajin prod_0-100ns.nc 6000 10000 200
molsurf A :LIG out LIG.dat

From literature, I obtained some reference values which I quote "The solvent accessible surface area of the ligand is reduced from 388 A^2 in the free state to 38 A^2 in the bound state”.

The results obtained using molsurf are way out. I obtained 220 A^2. My question is whether there’s something wrong with the script.

And an associated question relates to the Amber15 manual p. 739 which reads "to compute the solvent-accessible area, add the probe radius to each atom’s radius (using a for( a in m ) loop), and call molsurf with a zero value for probe_rad.”

As mbondi radii are included in my topology file, should I add in the last line of the script probe 0, i.e.
molsurf A :LIG out LIG.dat probe 0

If I use probe 0, the calculated SASA is ~250 A^2.

Thank you in advance for any suggestions


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Received on Thu Aug 27 2015 - 08:30:03 PDT
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