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
