Hi
you have to parametrize the atoms of the ligand. Here are two tutorials that might help you with this issue:
https://ambermd.org/tutorials/basic/tutorial4b/index.php
https://ambermd.org/tutorials/basic/tutorial19/index.php
I hope this pages solve you problem
________________________________
De: MD MUZAFFAR UR REHMAN via AMBER <amber.ambermd.org>
Enviado: viernes, 13 de octubre de 2023 7:32
Para: amber.ambermd.org <amber.ambermd.org>
Asunto: [AMBER] Error with tleap: Atom does not have a type
Dear All,
Please help me resolve this tleap error. Below is the error from tleap.log
file:
"> LIG1 = loadpdb _GMXMMPBSA_LIG_F1.pdb
Loading PDB file: ./_GMXMMPBSA_LIG_F1.pdb
Matching PDB residue names to LEaP variables.
/home/mb_uzair/miniconda3/envs/gmxMMPBSA/bin/teLeap: Warning!
Unknown residue: LIG number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
/home/mb_uzair/miniconda3/envs/gmxMMPBSA/bin/teLeap: Warning!
-no luck
Creating new UNIT for residue: LIG sequence: 900
Created a new atom named: O1 within residue: .R<LIG 900>
Created a new atom named: P1 within residue: .R<LIG 900>
Created a new atom named: C1 within residue: .R<LIG 900>
Created a new atom named: N1 within residue: .R<LIG 900>
Created a new atom named: C2 within residue: .R<LIG 900>
Created a new atom named: C3 within residue: .R<LIG 900>
Created a new atom named: C4 within residue: .R<LIG 900>
Created a new atom named: C5 within residue: .R<LIG 900>
Created a new atom named: C6 within residue: .R<LIG 900>
Created a new atom named: C7 within residue: .R<LIG 900>
Created a new atom named: C8 within residue: .R<LIG 900>
Created a new atom named: C9 within residue: .R<LIG 900>
Created a new atom named: C10 within residue: .R<LIG 900>
Created a new atom named: N2 within residue: .R<LIG 900>
Created a new atom named: P2 within residue: .R<LIG 900>
Created a new atom named: O2 within residue: .R<LIG 900>
Created a new atom named: O3 within residue: .R<LIG 900>
Created a new atom named: O4 within residue: .R<LIG 900>
Created a new atom named: O5 within residue: .R<LIG 900>
Created a new atom named: O6 within residue: .R<LIG 900>
total atoms in file: 20
The file contained 20 atoms not in residue templates
> LIG_OUT = combine { LIG1 }
Sequence: default_name
> saveamberparm LIG_OUT LIG.prmtop _GMXMMPBSA_LIG.inpcrd
Checking Unit.
FATAL: Atom .R<LIG 900>.A<O6 20> does not have a type.
FATAL: Atom .R<LIG 900>.A<O5 19> does not have a type.
FATAL: Atom .R<LIG 900>.A<O4 18> does not have a type.
FATAL: Atom .R<LIG 900>.A<O3 17> does not have a type.
FATAL: Atom .R<LIG 900>.A<O2 16> does not have a type.
FATAL: Atom .R<LIG 900>.A<P2 15> does not have a type.
FATAL: Atom .R<LIG 900>.A<N2 14> does not have a type.
FATAL: Atom .R<LIG 900>.A<C10 13> does not have a type.
FATAL: Atom .R<LIG 900>.A<C9 12> does not have a type.
FATAL: Atom .R<LIG 900>.A<C8 11> does not have a type.
FATAL: Atom .R<LIG 900>.A<C7 10> does not have a type.
FATAL: Atom .R<LIG 900>.A<C6 9> does not have a type.
FATAL: Atom .R<LIG 900>.A<C5 8> does not have a type.
FATAL: Atom .R<LIG 900>.A<C4 7> does not have a type.
FATAL: Atom .R<LIG 900>.A<C3 6> does not have a type.
FATAL: Atom .R<LIG 900>.A<C2 5> does not have a type.
FATAL: Atom .R<LIG 900>.A<N1 4> does not have a type.
FATAL: Atom .R<LIG 900>.A<C1 3> does not have a type.
FATAL: Atom .R<LIG 900>.A<P1 2> does not have a type.
FATAL: Atom .R<LIG 900>.A<O1 1> does not have a type.
/home/mb_uzair/miniconda3/envs/gmxMMPBSA/bin/teLeap: Fatal Error!
Failed to generate parameters
Exiting LEaP: Errors = 1; Warnings = 2; Notes = 0."
Kind Regards,
MD Muzaffar Ur Rehman,
*Research Scholar*
Department of Pharmacy
BITS-Pilani, Pilani campus, Rajasthan.
Alternate_email:
muzaffar.rehman.pilani.bits-pilani.ac.in
m.muzaffar687.gmail.com
Contact: +91-8686294437.
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Received on Mon Oct 16 2023 - 02:00:10 PDT
