AMBER Archive (2006)

Subject: Re: 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 - 10:43:18 CDT

Dear Harianto,

There is only one %FLAG RADII in the top file .... and all hydrogens
have 1.30000000E+00 radii, there isnt any 1.20000000E+00 number in my
top file so I dont know why ambpdb -pqr prints 1.200 for each H atom ...

ptraj, trajout dumpq works fine (I forgot about about it).... thanks

vlad

harianto wrote:

>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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-- 
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/

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