Re: [AMBER] [LEaP] Atom does not have a type

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Fri, 7 Feb 2020 11:02:01 -0500

Hi,
This structure has at least 2 residues (LYZ and HYP) that are not present
in the AMBER force field templates. Before trying to load it, you must
prepare parameters for them. I'd recommend you take a look into the AMBER
Tutorials here (http://ambermd.org/tutorials/), and especially the ones in
this list: http://ambermd.org/tutorials/ForceField.php.

All the best, 
--
Gustavo Seabra.
On Fri, Feb 7, 2020 at 9:10 AM Johannes Kalliauer <
johannes.kalliauer.tuwien.ac.at> wrote:
> Dear AmberUsers!
>
> I get the error
>
> > FATAL:  Atom .R<LYZ 0000>.A<CA 1> does not have a type.
> in leap.
>
> I read
> - http://archive.ambermd.org/201212/0122.html
> - http://archive.ambermd.org/201006/0253.html
> -
>
> https://www.researchgate.net/post/How_to_solve_Amber_Leap_PDB_preparation_error_atom_does_not_have_a_type
>
> but the problem persist, and I still don't understand how I can resolve
> the problem.
>
> How to reproduce the error:
>
> > #!/bin/bash
> >
> > #download PDB-file from https://www.rcsb.org/structure/3HR2
> > wget -O 3hr2.pdb  https://files.rcsb.org/download/3hr2.pdb
> >
> > tleap -f  ./Input.leap
> >
> with input.leap:
> > source leaprc.protein.ff14SB
> > source leaprc.water.tip3p
> > source leaprc.lipid17
> > source leaprc.gaff2
> > source leaprc.DNA.bsc1
> > source leaprc.DNA.OL15
> > source leaprc.protein.ff14SB
> >
> > COL1A1= loadpdb "3hr2.pdb"
> > saveamberparm COL1A1 COL1A1.prmtop COL1A1.inpcrd
> >
> I get following error-messages:
> > FATAL:  Atom .R<LYZ 103>.A<CA 1> does not have a type.
> > FATAL:  Atom .R<LYZ 700>.A<CA 1> does not have a type.
> > FATAL:  Atom .R<LYZ 934>.A<CA 1> does not have a type.
> > FATAL:  Atom .R<LYZ 946>.A<CA 1> does not have a type.
> > FATAL:  Atom .R<LYZ 1150>.A<CA 1> does not have a type.
> > FATAL:  Atom .R<LYZ 1171>.A<CA 1> does not have a type.
> > FATAL:  Atom .R<LYZ 1237>.A<CA 1> does not have a type.
> > FATAL:  Atom .R<LYZ 1282>.A<CA 1> does not have a type.
> > FATAL:  Atom .R<LYZ 1327>.A<CA 1> does not have a type.
> > FATAL:  Atom .R<LYZ 1711>.A<CA 1> does not have a type.
> > FATAL:  Atom .R<LYZ 1987>.A<CA 1> does not have a type.
> > FATAL:  Atom .R<LYZ 2183>.A<CA 1> does not have a type.
> > FATAL:  Atom .R<LYZ 2780>.A<CA 1> does not have a type.
> > FATAL:  Atom .R<LYZ 3014>.A<CA 1> does not have a type.
> > FATAL:  Atom .R<LYZ 3026>.A<CA 1> does not have a type.
> >
> > /home/jkalliau/prgm/amber18/bin/teLeap: Fatal Error!
> > Failed to generate parameters
>
> Hope for an answer, best Regards
> Johannes Kalliauer
> TU-Wien (Vienna)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Feb 07 2020 - 08:30:02 PST
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