Problem generating pdb psf of ATP

From: Srijita Paul (srijitap91_at_gmail.com)
Date: Mon May 14 2018 - 02:33:43 CDT

Hi,
I have a pdbfile(atp_namd.pdb) of ATP which is attached here which contains
ATP and Mg. I am trying to generate pdb and psf file of it using the
topology files mentioned below-
top_all36_cgenff.rtf
top_all36_na.rtf
toppar_all36_na_nad_ppi.str
toppar_water_ions.str

But after generating the pdb psf using psfgen I am getting a pdb which have
some wrong bond connectivy (atp_new.pdb).

What is the solution of the following problem?


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