Hi Stefano,
It's just what I want to do. I've never used Pybel before so I didn't know
this function. But I think that it will work for me. I'll try.
Thanks a lot.
Best wishes.
--
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http://forums.openbabel.org/Problem-in-converting-a-PDB-file-to-MOL2-tp4659035p46
Hi Stefano,
Thanks for the reply.
However, my problem is a bit different. It's more related to how to convert
a PDB to Mol2 considering the covalent bonds between the ligands and/or how
to get a SDF that represents a set of ligands covalently bonded.
Anyway, thank you.
best wishes.
--
View t
ds, each chemical compound that is deposited must have a
> unique ID, which
> will be in both the PDB and mmCIF files.
>
> Cheers,
>
> S
>
> On 11/20/2015 03:11 AM, Alexandre Fassio wrote:
>> Dimitri Maziuk wrote
>>> On 11/19/2015 05:07 PM, Alexandre Fassio
Dimitri Maziuk wrote
> On 11/19/2015 05:07 PM, Alexandre Fassio wrote:
>
> ... Apparently, they don't have a
>> ligand defined on the Chemical Component Dictionary that would represent
>> these assembled ligands.
>
> As I understand it, they'll make a separat
Dimitri Maziuk wrote
> On 2015-11-19 05:28, Alexandre Fassio wrote:
>
>> Right, it's true. But, for example, if I have 8 ligands covalently bonded
>> I
>> would like to consider these 8 ligands as it were only one ligand and
>> search
>> on the mmCIF dict
Pascal Muller-3 wrote
> Hi,
>
>
>
>> Right, it's true. But, for example, if I have 8 ligands covalently bonded
>> I
>> would like to consider these 8 ligands as it were only one ligand and
>> search
>> on the mmCIF dictionary for a ligand that represents the 8 ligands
>> together.
>> Because by
Dimitri Maziuk wrote
> On 2015-11-18 05:05, Alexandre Fassio wrote:
>
>> For example, a cellobiose can be represented as two glucoses (GLCs).
>> Thus,
>> it is difficult to know without a previous knowledge, which ligand is
>> represented by these two GLCs.
>>
Dimitri Maziuk wrote
> On 11/17/2015 01:14 PM, Alexandre Fassio wrote:
>
>> I've tried to use the mmCIF but I wasn't able to convert a ligand in the
>> mmCIF format to MOL2 by using Open Babel.
>>
>> For some reason that I don't know, I alw
Alexandre Fassio wrote
>
> Geoff Hutchison wrote
>>> Indeed, we've tried the SDF and it is a good option. However, some small
>>> ligands have covalent bonds with other small ligands and by using the
>>> SDF
>>> format we won't able to detec
Dimitri Maziuk wrote
> On 11/17/2015 10:34 AM, Alexandre Fassio wrote:
>
>> Indeed, we've tried the SDF and it is a good option. However, some small
>> ligands have covalent bonds with other small ligands and by using the SDF
>> format we won't able to de
Geoff Hutchison wrote
>> Indeed, we've tried the SDF and it is a good option. However, some small
>> ligands have covalent bonds with other small ligands and by using the SDF
>> format we won't able to detect it correctly.
>
> Can you give us some concrete examples of what you mean?
>
> -Geoff
>
Hi Pascal,
As I suspected the PDB file isn't suitable for my work since we need to
detect the correct valence of the atoms and its pharmacophore properties.
Indeed, we've tried the SDF and it is a good option. However, some small
ligands have covalent bonds with other small ligands and by using
Hi Pascal,
As I suspected the PDB file isn't suitable for my work since we need to
detect the correct valence of the atoms and its pharmacophore properties.
Indeed, we've tried the SDF and it is a good option. However, some small
ligands have covalent bonds with other small ligands and by using t
Hi there,
I tried to convert the ligand DDP from the format PDB to MOL2. This ligand
can be found in the PDB 1IL5.
However, Open Babel was not able to detect the aromatic atoms correctly. For
example, the nitrogen N1 was set as an amide (am) instead of aromatic (ar).
I suspect that convert a PDB
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