Hi Kajal,
it looks like you either have not loaded the phosphate residue definition
or more likely, since leap complains about only two atoms per phosphate
residue, there is a naming mismatch between the residue definition and the
pdb(?) input. Is there a chance your phosphate ion P and first O are named
"P1", "O1" vs "P", "O" in your inputs?
I'd recommend pasting the leap input and a description of what you did so
far into questions to this list, otherwise any help you receive will be at
best guesswork...
Kind Regards,
Thomas
On Sat, Aug 19, 2023 at 2:10 PM KAJAL ABROL via AMBER <amber.ambermd.org>
wrote:
> Dear AMBER community,
>
> After running tleap command, solvate.out file is showing the following
> error for phosphate ion:
>
> The file contained 20 atoms not in residue templates
> Checking Unit.
> FATAL: Atom .R<PO4 1821>.A<P 1> does not have a type.
> FATAL: Atom .R<PO4 1821>.A<O 2> does not have a type.
> FATAL: Atom .R<PO4 1822>.A<P 1> does not have a type.
> FATAL: Atom .R<PO4 1822>.A<O 2> does not have a type.
> FATAL: Atom .R<PO4 1823>.A<P 1> does not have a type.
> FATAL: Atom .R<PO4 1823>.A<O 2> does not have a type.
> FATAL: Atom .R<PO4 1824>.A<P 1> does not have a type.
> FATAL: Atom .R<PO4 1824>.A<O 2> does not have a type.
> FATAL: Atom .R<PO4 1825>.A<P 1> does not have a type.
> FATAL: Atom .R<PO4 1825>.A<O 2> does not have a type.
> FATAL: Atom .R<PO4 1826>.A<P 1> does not have a type.
> FATAL: Atom .R<PO4 1826>.A<O 2> does not have a type.
> FATAL: Atom .R<PO4 1827>.A<P 1> does not have a type.
> FATAL: Atom .R<PO4 1827>.A<O 2> does not have a type.
> FATAL: Atom .R<PO4 1828>.A<P 1> does not have a type.
> FATAL: Atom .R<PO4 1828>.A<O 2> does not have a type.
> FATAL: Atom .R<PO4 1829>.A<P 1> does not have a type.
> FATAL: Atom .R<PO4 1829>.A<O 2> does not have a type.
> FATAL: Atom .R<PO4 1830>.A<P 1> does not have a type.
> FATAL: Atom .R<PO4 1830>.A<O 2> does not have a type.
>
> amber22/bin/teLeap: Fatal Error!
> Failed to generate parameters
>
> Exiting LEaP: Errors = 1; Warnings = 21; Notes = 0.
>
>
> *Please suggest me any solution for rectifying this error. *
>
> Thanks and Regards,
> Kajal Abrol
> Research Scholar
> Department of Bioinformatics
> Pondicherry University
> Puducherry
> India
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Tue Aug 22 2023 - 01:30:02 PDT
