You could try deleting all hydrogens from your protein and then load it in
leap.
On Tuesday, June 30, 2020, Jatin Kashyap <jk435.njit.edu> wrote:
> Dear AMBER Users,
>
> I am trying to follow tutorials provided by one of the research group from
> Stony Brook University (http://ringo.ams.stonybrook.
> edu/index.php/2019_AMBER_tutorial_with_PDBID_2BXF).
>
> When I am using Tleap module and issues below commands[1] , It throws the
> following errors[2] :
>
> [1]
>
> ###Write Solvated topology and coord file
> saveamberparm solvcomplex 2BXF.wet.complex.prmtop 2BXF.wet.complex.rst7
>
>
>
> [2]
> Created a new atom named: HN within residue: .R<THR 304>
> Created a new atom named: HN within residue: .R<PHE 305>
> Created a new atom named: HN within residue: .R<CGLN 306>
> Added missing heavy atom: .R<CGLN 306>.A<OXT 18>
> total atoms in file: 2888
> Leap added 2096 missing atoms according to residue templates:
> 1 Heavy
>
> ….
> …
> ….
> FATAL: Atom .R<PHE 3>.A<HN 21> does not have a type.
> FATAL: Atom .R<GLY 2>.A<HN 8> does not have a type.
> FATAL: Atom .R<NSER 1>.A<HN3 16> does not have a type.
> FATAL: Atom .R<NSER 1>.A<HN2 15> does not have a type.
> FATAL: Atom .R<NSER 1>.A<HN1 14> does not have a type.
>
> /opt/amber/18/bin/teLeap: Fatal Error!
> Failed to generate parameters
>
> Exiting LEaP: Errors = 1; Warnings = 646; Notes = 0.
>
>
> Can anybody please help or provide any other tutorial to perform
> protein-ligand minimization.
> Thank you.
>
> ——
> Jatin Kashyap
>
>
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>
--
Best Regards
Elvis
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Received on Tue Jun 30 2020 - 00:30:04 PDT
