Hello,
On many molecules I am getting many warning for missing parameters when I
use Antechamber and the GAFF2 FF, but I also notice that the missing
parameters have been given GAFF parameters. Is this normal?
I just want to make sure I am doing this right since it feels wrong to be
getting so many errors/warnings.
Below is a sample for propylamine
Thanks,
Melania
-f: Source tleap.in.
Welcome to LEaP!
Sourcing: ./tleap.in
----- Source: /cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/amber/18/dat/leap/cmd/leaprc.gaff2
----- Source of /cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/amber/18/dat/leap/cmd/leaprc.gaff2
done
Log file: ./leap.log
Loading parameters: /cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/amber/18/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
Loading Mol2 file: ./PROPYLAMINE.mol2
Reading MOLECULE named MOL
Checking 'MOL'....
Checking parameters for unit 'MOL'.
Checking for bond parameters.
/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/amber/18/bin/teLeap:
Error!
Could not find bond parameter for: c3 - n8
/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/amber/18/bin/teLeap:
Error!
Could not find bond parameter for: n8 - hn
/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/amber/18/bin/teLeap:
Error!
Could not find bond parameter for: n8 - hn
Checking for angle parameters.
/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/amber/18/bin/teLeap:
Error!
Could not find angle parameter: c3 - c3 - n8
/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/amber/18/bin/teLeap:
Error!
Could not find angle parameter: c3 - n8 - hn
/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/amber/18/bin/teLeap:
Error!
Could not find angle parameter: c3 - n8 - hn
/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/amber/18/bin/teLeap:
Error!
Could not find angle parameter: h1 - c3 - n8
/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/amber/18/bin/teLeap:
Error!
Could not find angle parameter: h1 - c3 - n8
/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/amber/18/bin/teLeap:
Error!
Could not find angle parameter: hn - n8 - hn
/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/amber/18/bin/teLeap:
Warning!
There are missing parameters.
Unit is OK.
Loading parameters: ./PROPYLAMINE.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Building topology.
Building atom parameters.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 0 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
MOL 1
)
(no restraints)
Quit
Exiting LEaP: Errors = 9; Warnings = 1; Notes = 0.
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Received on Fri Jun 21 2019 - 23:30:02 PDT
