Re: readmol2 warning: non-unique atoms were renamed.

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Mon Jul 01 2019 - 15:12:29 CDT

Thank you for the clarification.

I will look into it

On Mon, Jul 1, 2019 at 7:42 PM Joao Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:

> Dear Adupa,
>
>
>
> 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.
>
>
>
> Best
>
>
>
> João
>
>
>
> *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.
>
>
>
> Thank you.
> --
>
>
> *A.VasistaM.Tech, Department Of Chemical Engineering,*
>
> *IIT Guwahati.*
>

-- 
*A.VasistaM.Tech,Department Of Chemical Engineering,*
*IIT Guwahati.*

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