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 - 04:30:02 PDT
