Hi Emma,
it would help to outline what you did and what your leap input looks like.
The error just shows that leap didnt recognize some residues in your
system. Based on the residue names, maybe you did not load the force field
parameters for water and ligands(?) X and L?
Typically this is caused by atom or residue naming mismatches, it's hard to
say more without more information.
Kind Regards,
Thomas
On Mon, Dec 18, 2023 at 12:02 AM Thompson, Emma via AMBER <amber.ambermd.org>
wrote:
> **Warning** The sender address ("Thompson, Emma via AMBER" ) can not be
> verified, sender email address could be spoofed. Please take care to
> proceed.
> Hello Amber users!
>
> I keep getting these errors when I run tleap and I am unsure how to fix
> them:
>
> FATAL: Atom .R<TIP 21746>.A<OH2 1> does not have a type.
> FATAL: Atom .R<X 21747>.A<KK 1> does not have a type.
> FATAL: Atom .R<L X 21748>.A<CL 1> does not have a type.
>
> I've looked at https://ambermd.org/tutorials/pengfei/index.php and
> https://github.com/choderalab/ambermini/blob/master/share/amber/dat/leap/cmd/leaprc.protein.ff14SB.
> I think they're helpful websites, but I am relatively new to this, so I am
> not sure what to do.
>
> Any thoughts/solutions?
>
> Thanks,
> Emma
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>
--
*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 Mon Dec 18 2023 - 01:30:03 PST
