In response to the message on the AMBER mailing list with the subject
line given above:
Regarding the comments with respect to FEW in this message:
> > As for the problem for using FEW,
> > A) If I use SDF file as the input of ligand structures, it
> will output a multiple-structure mol2 file. The error is:
> >
> > #####################################################
> > # #
> > # FEW #
> > # Free Energy Workflow #
> > # #
> > #####################################################
> >
> > Checking input parameters and files.
> >
> > ERROR: Problem in Babel conversion of sdf-format to mol2-format.
> Please consult the file
>
> > /home/zhonghua/disk/FEW/babel.log for details.
> > ~/babel.log:
> > 195 molecules converted
> > 2537 audit log messages
If the Babel log file contains only these two lines, there is likely no
problem in the conversion from SDF to MOL2. Please read the generated
MOL2 file into a structure editor and check whether the structures are
correct. FYI: FEW checks only if the size of the log file is > 0 bytes.
If this is the case, FEW outputs this error message. Likely in a
previous version of Babel no output was written into the log file, if no
errors were encountered. We will adapt FEW to the new Babel output, such
that the message above will only be displayed if Babel encounters
problems in the conversion.
>
> > B) if I use multiple-structure mol2 file converted from SDF file by
> Babel as the input, part of the error is:
> >
> > #####################################################
> > # #
> > # FEW #
> > # Free Energy Workflow #
> > # #
> > #####################################################
> >
> >
> > Checking input parameters and files.
> >
> > WARNING:
> > The residue name in the ligand file
> /home/zhonghua/disk/FEW/structs/Lig_ligprep_434.maegz:1.mol2
> > you provided is longer than three characters and will be shortened
> > to the first three characters.
> >
> > ERROR:
> > The atom names in the mol2-file
> /home/zhonghua/disk/FEW/structs/Lig_ligprep_434.maegz:1.mol2
> > are not unique. The atom name C is present at least twice.
> > Please ensure that the atom names in the ligand mol2-files are unique.
> >
> > As shown as all above, the residue name (more than 3 characters) and
> the atom name (without serial numbers) cannot be recognised by FEW.
>
FEW can handle residue names with more than 3-characters. This is only a
WARNING message to inform you that the residue name will be cut to
3-characters. This is not because FEW cannot handle longer names, but
because the files that are generated (e.g. PDB files) require residue
names that are not longer than 3-characters. The FEW setup should work
without any problem. Only the files that are gerated will containt the
first three characters of the residue name provided for the ligand
molecule as residue name. This is only relevant, if you would like to
analyze e.g. (outside of FEW) the generated trajectories with cpptraj
and would refer to the ligand molecule using its residue name. Other
than that, there should not be a problem in using longer residue names.
The ERROR messages appear because the atom names in the MOL2 file
generated by Babel upon conversion of the SDF to MOL2 format are not
unique. This message was included to make the user aware that the atom
names are not unique. This can especially cause problems, if a soft core
part is defined for TI, because the atom names will change upon setup in
order to ensure that the atom names are unique. For the MM-PBSA
calculations this should not matter and FEW should run correctly and you
should get a meaningful output despite the ERROR message. With respect
to consistency, it would be best if the atom names are unique in
general. You can create such an input file by writing a MOL2 file with
Maestro after ensuring that all atom names are unique using the maestro
editing -> atom labeling/naming options. The above problem arises from
the fact that only element names are written into the SDF files and
theses names are maintained upon conversion from SDF to MOL2. We will
try to provide a clearer ERROR message in the next FEW version and we
will provide additional information in the User's Manual.
Kind regards,
Nadine
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Received on Mon May 20 2019 - 11:30:02 PDT
