Dear List,
When I use OpenBabelGUI to split a multi-molecule file into individual pdbqt
files, each file starts with MODEL and ends with ENDMDL.
MODEL 2
REMARK Name = ZINC00001995
REMARK 5 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C_1 and C_2
REMARK 2 A between atoms: N_8 and C_19
.
..ENDBRANCH 8 19
TORSDOF 2
ENDMDL
This doesn't happen when I use command line OpenBabel using -m option.
REMARK Name = ZINC00001995
REMARK 5 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C_1 and C_2
REMARK 2 A between atoms: N_8 and C_19
...ENDBRANCH 8 19
TORSDOF 2
OpenBabelGUI uses molecule name for the individual files (e.g.
ZINC00001995.pdbqt), but command line OpenBabel requires a template name (e.g.,
new.pdbqt) and it generates files new1.pdbpt, new2.pdbqt, and so on. Is there
any way to ask OpenBabelGUI to avoid adding these two lines at the beginning
and end of the individual pdbqt files? Or alternatively, to use command line
OpenBabel in such a way to name the individual files based on the name of each
molecule in multi molecule file.
By the way, what is the option to add partial charges in command line OpenBable?
Yours,Siavoush
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