Re: [AMBER] Generating library from cif file.

From: David A Case <>
Date: Mon, 8 Mar 2021 11:31:40 -0500

On Mon, Mar 08, 2021, sriram raghavan wrote:

>I am trying to generate a residue library for a molecule called tomatine
>(mol2 file attached), I tried creating a "cif" restraint file using
>crystallographic tools (Jligand and phenix.elbow).
>I could generate a cif file but I am not able to process it with
>antechamber program

Lots of files have a .cif extension, but they may have different contents:

    1. Files from the PDB website called xxxx.cif contain the atomic model,
        and are roughly equivalent in content to the older xxxx.pdb files
    2. Files from the PDB website called xxxx-sf.cif containt structure
    3. The PDB site also has a file called "components.cif", which has
        information on all the non-protein, non-nucleic acid elments (aka
        residues) in the entire PDB.
    4. Crystallography programs make "restraint cif" files, that are only
        useful inside those programs.

Bottom line: you can't just look at the ".cif" extension and know what is
in the file. Antechamber can only read cif files of type 3, above. (Even
that is of limited usefulness: every entry in the components.cif file is
neutral, but many interesting ligands/residues are not. Antechamber doesn't
have the smarts to figure out the proper protonation state or tautomer.)

To create a residue library, you don't need or want a cif file. Just use
the mol2 file as input; better yet is to convert the mol2 to a PDB format,
and use that as input to antechamber.

...hope this helps...dac

AMBER mailing list
Received on Mon Mar 08 2021 - 09:00:03 PST
Custom Search