AMBER Archive (2006)

Subject: AMBER: printing Amber VdW radii as separate column in pdb files

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Mon Apr 10 2006 - 09:41:51 CDT

Dear amber users,

In the RADII section of the topology file, Born radii are printed (see
SECTION 1 below).... Now if I create a pqr file (ambpdb -pqr) from this
topology file I get on the radii column the output shown below in
SECTION 2. So, my first question is why the radii of the hydrogens are
different in the resulting pqr file comparing to the topology file...

And second question (actually the most important): Is there a way to
print out the VdW radii from the Amber ff (specified in the parm99.dat
lines 663 to 708) as a separate column in a pdb file created from an
AMBER top and crd files?

Thank you very much,

Best wishes
vlad

----------------------------------------------------------------------------------
SECTION 1:

%FLAG RADII
%FORMAT(5E16.8)
  1.55000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
  1.30000000E+00 1.30000000E+00 1.70000000E+00 1.50000000E+00 1.55000000E+00
---------------------------------------------------------------------------------
SECTION 2:

ATOM 1 N GLY 1 -22.774 -18.746 1.138 0.2943 1.550
ATOM 2 H1 GLY 1 -22.400 -17.825 0.958 0.1642 1.200
ATOM 3 H2 GLY 1 -23.230 -18.741 2.039 0.1642 1.200
ATOM 4 H3 GLY 1 -23.277 -19.057 0.319 0.1642 1.200
ATOM 5 CA GLY 1 -21.628 -19.693 1.281 -0.0100 1.700
ATOM 6 HA2 GLY 1 -21.698 -20.144 2.271 0.0895 1.200
ATOM 7 HA3 GLY 1 -21.746 -20.466 0.521 0.0895 1.200
ATOM 8 C GLY 1 -20.255 -19.050 1.125 0.6163 1.700
ATOM 9 O GLY 1 -19.242 -19.666 1.479 -0.5722 1.500
ATOM 10 N LYS 2 -20.225 -17.831 0.576 -0.4359 1.550
---------------------------------------------------------------------------------- 

-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu