Re: [AMBER] Fw: covalent molecule and modified residue parameters

From: David A Case <>
Date: Thu, 27 Aug 2020 21:03:23 -0400

On Thu, Aug 27, 2020, Sarah Jane wrote:
> Here is the antechamber command:antechamber -fi pdb -i HAR.pdb -fo mol2 -o
> HAR.mol2 -c bcc -nc 0 -at amber -s 2 -dr no

You HAR.pdb file has a very bad placement of the HO1 atom: it is only
1.6 from the CZ atom. I'm guessing that this is confusing to
antechamber, although the C=N double bond *could* be a problem.

Try rotating the HO1 above to point away from the rest of the molecule.

You also have mulitple unsatisfied valencies at the C and N atoms:
antechamber expects a complete moledule, not just an amino acid
fragment. You need to put capping groups on, run antehcamber, then take
the capping groups off.

Try this: go to, click on "tutorials and
examples", then on "generate residue topology files for non-standard
amino acids". (Apologies if you have already done this.....)

...good luck...dac

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Received on Thu Aug 27 2020 - 18:30:02 PDT
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