On Friday 04 July 2014 16:44:53 prasun
kumar wrote:
Thanks for your suggestion :D
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I think Pybel is just Open Babel for Python, which means there is no
different in the output between them. Anyway, I'll try to numbering the H
atoms incrementally. Thanks for your help :D.
On Fri, Jul 4, 2014 at 3:13 PM, Pascal Muller
wrote:
> Hi,
>
>
>> And what's your definition of "ligand" i
>
> Sorry, I was talking with my wife while writing, and that's not an option
> for this case :)
>
:))
And what's your definition of "ligand" in the PDB? :)
>
Well, it's on HETATM lines and not a familiar molecule like HOH or PO4 for
example.
Anyway, if you don't want to write a script to modif
APBS's requirement is that the atom should have different names, unless you
want it to ignore the duplications.
I can see that Babel adds number behind heavy atoms like C, O, etc. Why
doesn't it do so to H?
After searching for mol2 format of AB1, I have found this:
http://ligandbox.protein.osaka-
Hello Babel,
I would like Babel to have numbers in atom names when converting PDB to
MOL2. For example, this is a real output:
45 C369.9680 -15.9360 -13.8330 C.3 100 AB1100 -0.0362
46 C37 17.5010 -27.1690 -17.2360 C.3 100 AB1100 -0.0214
47 H
Well, I need the tag to convert the pdb format to pqr format by using
pdb2pqr program. The PRODGR server gives me that tag. Should I manually add
it to the mol2 file? It is:
@SUBSTRUCTURE
1 AB11
Does Open Babel add hydrogen with the AMBER force field? Or you don't need
force field to make a
.
Also, I would like to add H atoms to have them appear in mol2 output, with
AMBER99 force field. Do you have any suggestion for this?
Thank you.
Ooker.
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