Hello
I recently noted with the help of a colleague that atom names were not being
output properly after an OBminimization operation on a pdb file, especially one
that contains a Bromine atom.
The command I use is obminimize -ff UFF -sd -n 5000 -opdb ligand.pdb >
ligandMin.pdb
The input ligand
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
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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
You didn't say what version of OB or Ubuntu. Try the latest OB dev
version, and let us know if it doesn't work.
- Noel
On 16 November 2015 at 16:15, Osvaldo Martin wrote:
> I am trying to compile openbabel on Ubuntu (to make it work with python3)
> and I when I execute make I get the following e