Re: [AMBER] Amber prmtop and inpcrd of complex file with a water molecular cutoff

From: David A Case <>
Date: Thu, 9 Jul 2020 08:36:15 -0400

On Thu, Jul 09, 2020, 辛志宏 wrote:
>> mol = loadpdb DLP-499-cut-wat.pdb
>Loading PDB file: ./DLP-499-cut-wat.pdb
>-- residue 2048: duplicate [ H1] atoms (total 21)
>-- residue 2048: duplicate [ H2] atoms (total 21)

>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.)

This seems to me to be a pretty clear warning message: please examine residue
2048 in you structure to look for duplicate atom names.

>I wond how to correct the errors, thank you in advance.

FWIW: there were no errors in your email, just warnings. But the duplicate
atom name problem needs to be addressed.


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Received on Thu Jul 09 2020 - 06:00:05 PDT
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