Hi,
My guess is something is getting mangled when you read in the PDB (spacing,
name mismatch, etc) but someone else might know more- did you try deleting
everything but the backbone, renaming it ALA, and then letting tleap fill
in the missing atoms?
Best,
Kenneth
On Fri, Jul 30, 2021 at 7:10 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Dear All,
> I'm getting the following errors after mutating a Phe393 to Ala and there
> is no other change in the structure.
> The same set of parameters work perfectly well for the wild-type, thus I'm
> not sure why I'm getting this error. I did try using pdb4amber, and chimera
> to find Ala-CB coordinates, but in vain.
> All the missing atoms, angles and torsions parameters seem to be related to
> the protein chain (capital letters). Following are the tleap commands.
> Can you please help identify the route cause and suggest a fix to
> this issue?
> Looking forward to valuable suggestions from the list.
> thank you and best regards.
>
> (base) [exx.c107739 KACD-F393A-1BVY-FMN-sq-Fe3]$ tleap -s -f 1bvy_tleap.in
> -I: Adding /usr/local/amber18/dat/leap/prep to search path.
> -I: Adding /usr/local/amber18/dat/leap/lib to search path.
> -I: Adding /usr/local/amber18/dat/leap/parm to search path.
> -I: Adding /usr/local/amber18/dat/leap/cmd to search path.
> -s: Ignoring startup file: leaprc
> -f: Source 1bvy_tleap.in.
>
> Welcome to LEaP!
> Sourcing: ./1bvy_tleap.in
> ----- Source: /usr/local/amber18/dat/leap/cmd/leaprc.protein.ff14SB
> ----- Source of /usr/local/amber18/dat/leap/cmd/leaprc.protein.ff14SB done
> Log file: ./leap.log
> Loading parameters: /usr/local/amber18/dat/leap/parm/parm10.dat
> Reading title:
> PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
> Loading parameters: /usr/local/amber18/dat/leap/parm/frcmod.ff14SB
> Reading force field modification type file (frcmod)
> Reading title:
> ff14SB protein backbone and sidechain parameters
> Loading library: /usr/local/amber18/dat/leap/lib/amino12.lib
> Loading library: /usr/local/amber18/dat/leap/lib/aminoct12.lib
> Loading library: /usr/local/amber18/dat/leap/lib/aminont12.lib
> ----- Source: /usr/local/amber18/dat/leap/cmd/leaprc.gaff
> ----- Source of /usr/local/amber18/dat/leap/cmd/leaprc.gaff done
> Log file: ./leap.log
> Loading parameters: /usr/local/amber18/dat/leap/parm/gaff.dat
> Reading title:
> AMBER General Force Field for organic molecules (Version 1.81, May 2017)
> Loading Mol2 file:
> /home/exx/Documents/CYP450-BM3/1BVY/NPG-MD-1BVY-FMN-sq-Fe3/CM1.mol2
> Reading MOLECULE named CM1
> Loading Mol2 file:
> /home/exx/Documents/CYP450-BM3/1BVY/NPG-MD-1BVY-FMN-sq-Fe3/HM1.mol2
> Reading MOLECULE named HM1
> Loading Mol2 file:
> /home/exx/Documents/CYP450-BM3/1BVY/NPG-MD-1BVY-FMN-sq-Fe3/FE1.mol2
> Reading MOLECULE named FE1
> Loading Mol2 file:
> /home/exx/Documents/CYP450-BM3/1BVY/NPG-MD-1BVY-FMN-sq-Fe3/FMN-sq-H.mol2
> Reading MOLECULE named FMN
> Loading Mol2 file: ../KACD-MD-1BVY-FMN-sq-Fe3/ACD-2.mol2
> Reading MOLECULE named LIG
> Loading parameters: ../KACD-MD-1BVY-FMN-sq-Fe3/ACD-2.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> Remark line goes here
> Loading parameters:
> /home/exx/Documents/CYP450-BM3/1BVY/NPG-MD-1BVY-FMN-sq-Fe3/HEM.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> Remark line goes here
> Loading parameters:
>
> /home/exx/Documents/CYP450-BM3/1BVY/NPG-MD-1BVY-FMN-sq-Fe3/4ZF6_mcpbpy.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> REMARK GOES HERE, THIS FILE IS GENERATED BY MCPB.PY
> Loading parameters:
> /home/exx/Documents/CYP450-BM3/1BVY/NPG-MD-1BVY-FMN-sq-Fe3/FMN-sq-H.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> Remark line goes here
> ----- Source: /usr/local/amber18/dat/leap/cmd/leaprc.water.opc
> ----- Source of /usr/local/amber18/dat/leap/cmd/leaprc.water.opc done
> Loading library: /usr/local/amber18/dat/leap/lib/atomic_ions.lib
> Loading library: /usr/local/amber18/dat/leap/lib/solvents.lib
> Loading parameters: /usr/local/amber18/dat/leap/parm/frcmod.opc
> Reading force field modification type file (frcmod)
> Reading title:
> Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871)
> Loading parameters: /usr/local/amber18/dat/leap/parm/frcmod.ionsjc_tip4pew
> Reading force field modification type file (frcmod)
> Reading title:
> Monovalent ion parameters for Ewald and TIP4P/EW water from Joung &
> Cheatham JPCB (2008)
> Loading parameters:
> /usr/local/amber18/dat/leap/parm/frcmod.ions234lm_126_tip4pew
> Reading force field modification type file (frcmod)
> Reading title:
> Li/Merz ion parameters of divalent to tetravalent ions for TIP4P/EW water
> model (12-6 normal usage set)
> Loading PDB file: ./1bvy-af-ACD-F393A-2.pdb
> Added missing heavy atom: .R<ALA 374>.A<CB 5>
>
> /usr/local/amber18/bin/teLeap: Warning!
> One sided connection. Residue (CM1) missing connect0 atom.
> total atoms in file: 9743
> Leap added 9 missing atoms according to residue templates:
> 1 Heavy
> 8 H / lone pairs
> Writing pdb file: 1bvy-af-ACD-F393A-dry.pdb
>
> /usr/local/amber18/bin/teLeap: Warning!
> Converting N-terminal residue name to PDB format: NLEU -> LEU
>
> /usr/local/amber18/bin/teLeap: Warning!
> Converting N-terminal residue name to PDB format: NILE -> ILE
>
> /usr/local/amber18/bin/teLeap: Warning!
> Converting C-terminal residue name to PDB format: CLEU -> LEU
> Checking Unit.
>
> /usr/local/amber18/bin/teLeap: Warning!
> There is a bond of 3.483386 angstroms between:
>
> /usr/local/amber18/bin/teLeap: Warning!
> There is a bond of 7.922807 angstroms between:
>
> /usr/local/amber18/bin/teLeap: Warning!
> The unperturbed charge of the unit (-28.001999) is not zero.
>
> /usr/local/amber18/bin/teLeap: Note.
> Ignoring the warnings from Unit Checking.
> Building topology.
> Building atom parameters.
> Building bond parameters.
>
> /usr/local/amber18/bin/teLeap: Error!
> Could not find bond parameter for: C - N3
> Building angle parameters.
>
> /usr/local/amber18/bin/teLeap: Error!
> Could not find angle parameter: O - C - N3
>
> /usr/local/amber18/bin/teLeap: Error!
> Could not find angle parameter: C - N3 - H
>
> /usr/local/amber18/bin/teLeap: Error!
> Could not find angle parameter: C - N3 - H
>
> /usr/local/amber18/bin/teLeap: Error!
> Could not find angle parameter: C - N3 - H
>
> /usr/local/amber18/bin/teLeap: Error!
> Could not find angle parameter: C - N3 - CX
>
> /usr/local/amber18/bin/teLeap: Error!
> Could not find angle parameter: CX - C - N3
> Building proper torsion parameters.
>
> /usr/local/amber18/bin/teLeap: Error!
> ** No torsion terms for O-C-N3-H
>
> /usr/local/amber18/bin/teLeap: Error!
> ** No torsion terms for O-C-N3-H
>
> /usr/local/amber18/bin/teLeap: Error!
> ** No torsion terms for O-C-N3-H
>
> /usr/local/amber18/bin/teLeap: Error!
> ** No torsion terms for O-C-N3-CX
>
> /usr/local/amber18/bin/teLeap: Error!
> ** No torsion terms for CX-C-N3-H
>
> /usr/local/amber18/bin/teLeap: Error!
> ** No torsion terms for CX-C-N3-H
>
> /usr/local/amber18/bin/teLeap: Error!
> ** No torsion terms for CX-C-N3-H
>
> /usr/local/amber18/bin/teLeap: Error!
> ** No torsion terms for CX-C-N3-CX
> Building improper torsion parameters.
> total 1983 improper torsions applied
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
>
> /usr/local/amber18/bin/teLeap: Warning!
> Parameter file was not saved.
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> NCBI bibliography:
> https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
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Received on Fri Jul 30 2021 - 07:30:02 PDT
