Dear Wes,
I load a molecule by its prmtop and inpcrd file (produced in Amber Tools 12) in VMD. Then I go to ‘VMD main’ menu to ‘File’ to ‘New Molecule..’ to ‘Molecule File Browser’ . Then select ‘New Molecule’ in ‘Load Files For:’ section, brows the pbsa.dx file and open it then hit the ‘Load’ button and the same times the ‘determine file type:’ was in ‘DX’ form. Then I see a picture in VMD 1.8.6 Open GL display. The molecule is in box and the potential data arises as dots, surrounded the molecule. Then I go to ‘VMD Main’ menu to ‘Graphics’ to ‘Graphical Representation’ then select the ‘.prmtop’ from ‘Selected molecule’ section. Then go back to the ‘VMD Main’ menu to ‘Extensions’ to ‘Tk Console’. A window is appeared as ‘VMD TkConsole’ which contain the following dilog-
Main console display active (Tcl8.4.1 / Tk8.4.1)
(VMD) 1 %
Then I write the command given in the Amber Tools 12 in section 8.4.12 which as follows (does not hit enter)-
Main console display active (Tcl8.4.1 / Tk8.4.1)
(VMD) 1 % set prot [atomselect "top" all] $prot set radius {#RadiiList#}
Then I copy the Radii from prmtop file under the flag %FLAG RADII and %FORMAT(5E16.8). It was as follows-
8.00000000E-01 1.50000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00
1.70000000E+00 1.30000000E+00 1.50000000E+00 1.70000000E+00 1.30000000E+00
1.55000000E+00 1.70000000E+00 1.30000000E+00 1.55000000E+00 1.70000000E+00
…………………………………………………………
…………………………………………………………
1.70000000E+00 1.30000000E+00 1.50000000E+00 8.00000000E-01 1.50000000E+00
8.00000000E-01
Then pest this numbers in the #RadiiList# position. So the number placed with in a 2nd bracket. Then hit the enter button. The following message is appeared in ‘VMD TkConsole’ window-
can't read "prot": no such variable
>Main< (VMD) 2 %
Have I make any mistake? Please let me know.
Best regards,
Sudarshan
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Received on Thu May 24 2012 - 04:30:03 PDT
