HI
I would particularly look at these warnings
/opt/amber/20/bin/teLeap: Warning!
There is a bond of 4.431221 angstroms between:
>> Did you forget to put a "TER" between protein chains? look at the
structure closely, there is something wrong here.
/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.
> I would delete all protein hydrogens before feeding them to leap.
try "reduce -Trim" command
/opt/amber/20/bin/teLeap: Fatal Error!
Failed to generate parameters
Best Regards
Elvis
On Sat, 29 Aug 2020 at 11:17, Jatin Kashyap <jk435.njit.edu> wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
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>
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Received on Fri Aug 28 2020 - 23:30:02 PDT
