It looks like your ligand is not parameterized or somehow misnamed.
Check out the Amber tutorials on building systems and parameterizing
non-standard residues here:
https://ambermd.org/tutorials/
especially 1.1, 1.2, 2.1 and 2.2 look relevant to your system.
Kind Regards,
Thomas
On Fri, Oct 13, 2023 at 7:33 AM MD MUZAFFAR UR REHMAN via AMBER <
amber.ambermd.org> wrote:
> **Warning** The sender address (MD MUZAFFAR UR REHMAN via AMBER ) can not
> be verified, sender email address could be spoofed. Please take care to
> proceed.
> 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 Fri Oct 13 2023 - 00:00:03 PDT
