Re: [AMBER] MD on small molecules, The file contained 8 atoms not in residue templates

From: David Case <>
Date: Wed, 21 Aug 2019 02:29:47 +0000

On Sat, Aug 10, 2019, Amen Shamim wrote:

>UNK=loadmol2 mol1.mol2

This command is not doing what you may think it is doing. Type "help
loadMol2" at the tleap command line. Note that is says this: "The UNIT
loaded will have the name specified for the MOLECULE in the input file."
So the "UNK=" part of the command is not specifying the name of the unit
that is created.

>> pdb=loadpdb solvprotein.pdb
>Loading PDB file: ./solvprotein.pdb
>-- residue 1: duplicate [ C] atoms (total 2)
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)

You should figure out why you have duplicate atom names in

>Created a new atom named: O within residue: .R<UNK 1>

This means that UNK does describe the molecule you think it does. Use
the "desc" command in tleap to see what is actually inside each unit.
But it seems likely(?) that the command at the top of this email may be
the cause of the problem.


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Received on Tue Aug 20 2019 - 19:30:04 PDT
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