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

From: Johannes Kalliauer <johannes.kalliauer.tuwien.ac.at>
Date: Fri, 7 Feb 2020 15:09:29 +0100

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)



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Received on Fri Feb 07 2020 - 06:30:03 PST
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