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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Received on Tue Jun 30 2020 - 00:30:03 PDT
