AMBER Archive (2006)

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

From: harianto (harianto_at_mailer.sb.fsu.edu)
Date: Mon Apr 10 2006 - 10:12:39 CDT

Dear Vlad,
By default, "ambpdb -pqr" command prints the 'PBRadii Bondi' set, but in
your top file they look like 'PBradii mBondi2'.
You can use ptraj option 'trajout file.out PDB [dumpq/PARSE]', for
example, to print out the PDB with radii and charge columns.
Does that help ?

Regards,
Harianto.

On Mon, 2006-04-10 at 16:41 +0200, Vlad Cojocaru wrote:
> 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
> ----------------------------------------------------------------------------------

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