From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Sat Jun 29 2019 - 11:30:25 CDT
I have drawn a Ligand in Avogadro. When I run Autopsf normal parameter
files are not able to recognize these Atom types, so I uploaded the
molecule in cgenff.it gave me a warning "*readmol2 warning: non-unique
atoms were renamed".*
I checked the PDB its atom type is UNK / LIG. Do I need to change the atom
despite the warning message, cgenff is able to generate a parameter file
but when I use the parameter file and run Autopsf and load autopsf
generated psf and pdb, I am not able to see my ligand in VMD.
Here I attach the PDB of the ligand.
-- *A.VasistaM.Tech, Department Of Chemical Engineering,* *IIT Guwahati.*
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