[AMBER] "FATAL: Atom *** does not have a type" Error

From: Jatin Kashyap <jk435.njit.edu>
Date: Sat, 29 Aug 2020 01:44:11 -0400

Dear AMBER Community,

I am trying to perform MD run on a ligand-receptor complex after splitting and preparing them individually in PyMol from a RCSB downloaded version.
My job is getting stuck with a fatal error. I am pasting below the content of the log file. I had noticed that something is wrong with protein file as AMBER is generating extra atoms in it when I am loading it in. And then those atoms are creating errors which halted the job.

Can anybody please help me to understand what I am doing wrong here.

Thank you very much.

###Load Protein pdb file
> rec=loadpdb ../zzz.master/2nnq.rec.withH.charged.pdb
Loading PDB file: ../zzz.master/2nnq.rec.withH.charged.pdb
Matching PDB residue names to LEaP variables.
Mapped residue CYS, term: Terminal/beginning, seq. number: 0 to: NCYS.
Mapped residue ALA, term: Terminal/last, seq. number: 129 to: CALA.
Created a new atom named: HA2 within residue: .R<GLU 54>
Created a new atom named: HA3 within residue: .R<GLU 54>
  Added missing heavy atom: .R<GLU 54>.A<CB 5>
  Added missing heavy atom: .R<GLU 54>.A<CG 8>
  Added missing heavy atom: .R<GLU 54>.A<CD 11>
  Added missing heavy atom: .R<GLU 54>.A<OE1 12>
  Added missing heavy atom: .R<GLU 54>.A<OE2 13>
Created a new atom named: HG1 within residue: .R<LYS 79>
  Added missing heavy atom: .R<LYS 79>.A<CD 11>
  Added missing heavy atom: .R<LYS 79>.A<CE 14>
  Added missing heavy atom: .R<LYS 79>.A<NZ 17>
  total atoms in file: 2020
  Leap added 20 missing atoms according to residue templates:
       8 Heavy
       12 H / lone pairs
  The file contained 3 atoms not in residue templates
> ###Load Ligand frcmod/mol2
> loadamberparams ../000.programs/2nnq_lig.am1bcc.frcmod
Loading parameters: ../000.programs/2nnq_lig.am1bcc.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> lig=loadmol2 ../000.programs/2nnq_lig.am1bcc.mol2
Loading Mol2 file: ../000.programs/2nnq_lig.am1bcc.mol2
Reading MOLECULE named LIG
> ###Create gas-phase complex
> gascomplex= combine {rec lig}
  Sequence: default_name
  Sequence: LIG
> ###Write gas-phase pdb
> savepdb gascomplex 2nnq.gas.complex.pdb
Writing pdb file: 2nnq.gas.complex.pdb

/opt/amber/20/bin/teLeap: Warning!
 Converting N-terminal residue name to PDB format: NCYS -> CYS

/opt/amber/20/bin/teLeap: Warning!
 Converting C-terminal residue name to PDB format: CALA -> ALA
> ###Write gas-phase toplogy and coord files for MMGBSA calc
> saveamberparm gascomplex 2nnq.gas.complex.prmtop 2nnq.gas.complex.rst7
Checking Unit.

/opt/amber/20/bin/teLeap: Warning!
There is a bond of 4.431221 angstroms between:

/opt/amber/20/bin/teLeap: Warning!
The unperturbed charge of the unit (-1.999001) is not zero.
FATAL: Atom .R<LYS 79>.A<HG1 23> does not have a type.
FATAL: Atom .R<GLU 54>.A<HA3 17> does not have a type.
FATAL: Atom .R<GLU 54>.A<HA2 16> does not have a type.

/opt/amber/20/bin/teLeap: Fatal Error!
Failed to generate parameters

Exiting LEaP: Errors = 1; Warnings = 4; Notes = 0.

Jatin Kashyap
Ph.D. Student
Dr. Dibakar Datta Group
Department of Mechanical and Industrial Engineering
New Jersey Institute of Technology (NJIT)
University Heights
Newark, NJ 07102-1982
Phone- (201)889-5783
Email- jk435.njit.edu

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Received on Fri Aug 28 2020 - 23:00:03 PDT
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