Re: [AMBER] -Antechamber error for modified residues

From: David Case <>
Date: Sat, 28 Sep 2019 12:44:55 +0000

On Thu, Sep 26, 2019, Patil Pranita Uttamrao wrote:

>I am trying to prepare the residue library and force field parameters of
>the modified residue G7M(.cif attached) using antechamber as given below.
>$ antechamber -fi ccif -i G7M.cif -bk G7M -fo ac -o -c bcc -at amber

Pulling a block from components.cif generally won't work for modified
residues (just for non-covalent ligands.) The PDB add hydrogens to make
all components neutral -- this is generally not what you want, so
hand-editing of these files is usually needed.

See for basic
instructions on preparing a modified residue: you need to add capping
groups, do the quantum charge calculation, then remove the capping

Note also that starting parameters for 7-methyl-guanosine are already
available for Amber: see the all_modrna08.lib and related files.

....good luck....dac

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Received on Sat Sep 28 2019 - 06:00:04 PDT
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