[AMBER] assignment of partial charge to fullerene2160

From: gargi borgohai <gargib2011.gmail.com>
Date: Tue, 27 Mar 2012 12:45:21 +0530

Respected Sir,
                    I am trying to generate polar confinement using
fullerene2160. To do so I assigned some charge values ( both positive
(+0.15e) and negative (-0.15e) so that ultimate charge of the molecule
becomes zero) to the mol2 file. Then I loaded the mol2 file at XLEaP and
saved the .prmtop and .inpcrd files. After that when I minimised the
structure and saved the pdb file in order to visualize the structure with
VMD then the structure showed that all carbon atoms are detached from each
other i.e. fullerene ball contained only carbon atoms and not any bond. The
input file I used for minimization:

initial minimization of complete system

Sir I am not able to find whether there is any wrong with my input file or
charge assignment method. I will be thankful if you let me know how can I
add partial charges to the fullerene ball successfully.
Thanking you.


Gargi Borgohain
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Received on Tue Mar 27 2012 - 00:30:03 PDT
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