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.
--
View this message in context:
http://forums.openbabel.org/Problem-in-converting-a-PDB-file-to-MOL2-tp4659035p46
Hi Alexandre,
assuming that I now understand what you want to do, you could extract/process
each
separate ligand generating individuals OBMol objects, then you can combine them
into a
single molecule, i.e. (Python):
full = openbabel.OBMol()
for frag in fragments:
full += frag
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
Stefano Forli wrote
> Hi,
> I don't know if it can be useful for this specific problem, but the PDB
> has an advanced
> search interface which allows to use chemical information to query
> structures:
>
>http://www.rcsb.org/pdb/search/advSearch.do?search=new
>Choose a Query Type -> Chemic
Hi,
I don't know if it can be useful for this specific problem, but the PDB has an
advanced
search interface which allows to use chemical information to query structures:
http://www.rcsb.org/pdb/search/advSearch.do?search=new
Choose a Query Type -> Chemical component: ...
You can use SMIL
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 separate "compound" ligand for things
> that
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 separate "compound" ligand for things
that they see often, like in drugs -- I
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 dictionary for a ligand that represents the 8 l
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
On 11/19/2015 10:17 AM, Dimitri Maziuk wrote:
> I think our best option
--^^^
That was supposed to be "your"
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
signature.asc
Description: OpenPGP digital signature
--
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 dictionary for a ligand that represents the 8 ligands together.
> Because by sear
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 searching an ID for each ligand separat
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.
>>
>> In another case, I had a PDB with
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.
>
> In another case, I had a PDB with 8 ligands covalently bonded and I
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 always got the message "0 molecules
>> converted".
>
> Lik
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 always got the message "0 molecules
> converted".
Like I said, I don't know of any soft
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 detect it correctly.
>>
>> Can you give us some concrete exam
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 detect it correctly. If you have any suggesti
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
>
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 detect it correctly. If you have any suggestion,
> it'll be welcome.
If
> 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,
>
> 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 conv
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
25 matches
Mail list logo
