[apbs-users] PQR file for Ca2+

[Mendez Giraldez, Raul]

Dear all,

Does any one know how to generate PQR file for Ca2+ ion ? I have seen some PDB2PQR forums suggesting CHARMM radius for Ca2+, which is 1.367 angstroms, other people suggest AMBER radius 1.7131 angstroms, and I thought that it should be the Born Radius, which is 1.862.

Which one would you use ?

Thanks.

Raul

Raul Mendez Giraldez, PhD

Dokholyan Lab

Dept. Biophysics & Biochemistry 

Genetic Medicine

University of North Carolina

120 Mason Farm Road

Chapel Hill, NC 27599

US

[Baker, Nathan]

Hi Raul --

Calcium solvation is not described very well by implicit solvent models so I would exercise caution for whatever model you use.  That being said, for the purposes of electrostatics and solvation calculations (not molecular mechanics), I would recommend using the Born radius.

Caveat emptor.

Thanks,

--
Nathan Baker
Laboratory Fellow and Technical Group Manager
Applied Statistics and Computational Modeling
Pacific Northwest National Laboratory
+1-509-375-3997
http://www.linkedin.com/in/nathanandrewbaker

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From: Mendez Giraldez, Raul [rme...@email.unc.edu]
Sent: Wednesday, November 12, 2014 12:55
To: apbs-...@lists.sourceforge.net
Subject: [apbs-users] PQR file for Ca2+