From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Mon Jul 01 2019 - 09:12:22 CDT
The problem is not the atoms’ type, but the atoms’ name. Atom’s type doesn’t need to be unique in the sense that atom’s sharing the same characteristics, ought to share the same atom type. On the other hand, the atom’s name must be unique as two atoms cannot share the same name. In your case, the atoms were named with their element, which forced them to have the same name.
If you check you topology file returned by CGenFF, you will see that the atoms name are different, and the PDB file needs to match these names.
From: <owner-namd-l_at_ks.uiuc.edu> on behalf of Adupa Vasista <adupavasista_at_gmail.com>
Reply-To: <namd-l_at_ks.uiuc.edu>, Adupa Vasista <adupavasista_at_gmail.com>
Date: Saturday, June 29, 2019 at 11:38 AM
To: NAMD list <namd-l_at_ks.uiuc.edu>
Subject: namd-l: readmol2 warning: non-unique atoms were renamed.
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 type?
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.Vasista M.Tech, Department Of Chemical Engineering, IIT Guwahati.
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