Re: [Open Babel] error compiling openbabel

[Noel O'Boyle]

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 error:
>
> error: ‘std::tr1’ has not been declared
>
> Cheers,
> Osvaldo.
>
>
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Re: [Open Babel] Problem in converting a PDB file to MOL2

[Dimitri Maziuk]

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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Re: [Open Babel] Problem in converting a PDB file to MOL2

[Dimitri Maziuk]

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 can't provide an example off the
top of my head I'm afraid. For most "one-off" cases they will have them
as separate ligands. But there should still be information in the
struct_conn table in mmCIF for the macro structure.

There's also chem_comp_atom.leaving_atom_flag in the ligand mmCIF, but
that one's an even worse mess. :(

-- 
Dimitri Maziuk
Programmer/sysadmin
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[Open Babel] atom names stripped in OBminimize

[Bennion, Brian]

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 looks like this.

REMARK  LIG
ATOM  1  O1  LIG 1   5.811  -0.667  -1.538
ATOM  2  C1  LIG 1   5.526  -0.301  -0.356
ATOM  3  C2  LIG 1   6.376  -0.204   0.681
ATOM  4  N1  LIG 1   7.739  -0.535   0.487
ATOM  5  O2  LIG 1   8.391  -0.399   1.516
ATOM  6  N2  LIG 1   4.154   0.022  -0.194
ATOM  7  C3  LIG 1   3.472   0.290   1.081
ATOM  8  C4  LIG 1   1.966   0.316   0.783
ATOM  9  C5  LIG 1   1.902   0.770  -0.676
ATOM 10  N3  LIG 1   0.653   0.271  -1.375
ATOM 11  C6  LIG 1  -0.500   1.269  -1.393
ATOM 12  C7  LIG 1  -1.071   1.580   0.008
ATOM 13  Br1 LIG 1  -2.451   2.974  -0.194

After minimization I have this:
REMARKLIG
COMPNDUNNAMED
AUTHORGENERATED BY OPEN BABEL 2.3.2
HETATM1  O   LIG 1   5.910  -0.355  -1.445  1.00  0.00   O
HETATM2  C   LIG 1   5.473  -0.035  -0.347  1.00  0.00   C
HETATM3  C   LIG 1   6.424   0.152   0.808  1.00  0.00   C
HETATM4  N   LIG 1   7.798  -0.131   0.417  1.00  0.00   N
HETATM5  O   LIG 1   8.544  -0.115   1.547  1.00  0.00   O
HETATM6  N   LIG 1   4.130   0.144  -0.177  1.00  0.00   N
HETATM7  C   LIG 1   3.523   0.507   1.080  1.00  0.00   C
HETATM8  C   LIG 1   2.043   0.231   0.823  1.00  0.00   C
HETATM9  C   LIG 1   1.898   0.610  -0.655  1.00  0.00   C
HETATM   10  N   LIG 1   0.674   0.122  -1.330  1.00  0.00   N
HETATM   11  C   LIG 1  -0.498   1.020  -1.251  1.00  0.00   C
HETATM   12  C   LIG 1  -1.106   1.221   0.159  1.00  0.00   C
HETATM   13  B   LIG 1  -2.254   2.326   0.069  1.00  0.00   B

Am I doing something incorrect?

Thanks
Brian Bennion

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Re: [Open Babel] Problem in converting a PDB file to MOL2

[Alexandre Fassio]

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 searching an ID for each ligand separately I wouldn't be
>> considering the covalent bonds between them.
>>
>>
> You may try PDBsum. On the ligand page for 1h4p
> (NAG-NAG-BMA-BMA-MAN-BMA-MAN-MAN-BMA-BMA), you will find this file (link
> in
> picture sphere above jmol logo) :
> http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/RunRomLas.pl?pdb=1h4p_02_01=pdbsum=YES=-l_atoms=YES
> 
> This file seems to contain the structure of the full ligand - but
> unfortunately in PDB format, with some CONECT at least.
> 
> Otherwise, the cif file of 1h4p seems to contain all the needed
> information
> too.
> E.g. look for _pdbx_nonpoly_scheme.asym_id in
> http://www.rcsb.org/pdb/files/1H4P.cif : the asym_id G is only for the
> ligand NAG-NAG-BMA-BMA-MAN-BMA-MAN-MAN-BMA-BMA. Unfortunately, I'm not
> familiar enough yet with the mmcif format for additional hint, but I think
> you can get somehow the full ligand with the mmcif file.
> But anyway you will need many fixes to get the correct ligands structure
> for such tricky cases, as for the occupancy problem.
> 
> You could try the CCL list too for this question.
> 
> I hope it helps a bit :)
> 
> Regards,
> Pascal
> 
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Hi Pascal,

Thanks for the reply.

I tried the PDBSum today to test what you mentioned. Unfortunately, the
PDBSum seems to have only PDB files formats to download. Moreover, both the
PDB and the CIF are not so suitable for me because I need to convert the
file to MOL2 and I think that these formats could generate some errors after
the conversion with Open Babel due to the lack of charge, valence, bond
order information, etc (correct if I'm wrong).

Anyway, the PDBSum gave some insights and I liked the way that they treat
the covalently bonded ligands.

Thanks for the help.



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Re: [Open Babel] Problem in converting a PDB file to MOL2

[Alexandre Fassio]

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 ligands
>> together.
>> Because by searching an ID for each ligand separately I wouldn't be
>> considering the covalent bonds between them.
> 
> I think our best option is to e-mail e.g. 

> deposit@.rcsb

>  or 
> whatever other help address they have (deposit is the one for people 
> submitting structures -- but they will forward your question to the 
> right people) and ask "how do I find all entries containing e.g.
> NAG-NAG-BMA-BMA-MAN-BMA-MAN-MAN-BMA-BMA" sequence.
> 
> Dimitri
> 
> 
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Hi Dimitri,

Alright, this is an option too. Meanwhile, I think that the best option is
to evaluate each ligand separately. 

After checking on PDBSum as Pascal has suggested to me, I saw that the 8
ligands I had mentioned before are considered as a ligand called
"NAG-NAG-BMA-BMA-MAN-BMA-MAN-MAN-BMA-BMA". Apparently, they don't have a
ligand defined on the Chemical Component Dictionary that would represent
these assembled ligands.

Maybe, the only way to evaluate these ligands will be analysing one by one
separately.

Thank you a lot.

Alexandre




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Re: [Open Babel] Problem in converting a PDB file to MOL2

[Alexandre Fassio]

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 8 ligands covalently bonded and I don't
>> know which ligand in the CIF dictionary represents these 8 ligands.
> 
> Well, if you download an mmCIF for the ligand, 
> _chem_comp.pdbx_subcomponent_list field should contain the 3-letter 
> codes. I don't know if they've gone through their entire ligand library 
> and filled in that field in every "compound component", though.
> 
> E.g. in some cases, like ALA_NH2, they list NH2 as a separate chem. 
> comp. instead.
> 
> Dimitri
> 
> 
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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 separately I wouldn't be
considering the covalent bonds between them.



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Re: [Open Babel] Problem in converting a PDB file to MOL2

[Dimitri Maziuk]

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 searching an ID for each ligand separately I wouldn't be
> considering the covalent bonds between them.

I think our best option is to e-mail e.g. depo...@deposit.rcsb.org or 
whatever other help address they have (deposit is the one for people 
submitting structures -- but they will forward your question to the 
right people) and ask "how do I find all entries containing e.g.
NAG-NAG-BMA-BMA-MAN-BMA-MAN-MAN-BMA-BMA" sequence.

Dimitri


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Re: [Open Babel] Problem in converting a PDB file to MOL2

[Pascal Muller]

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 separately I wouldn't be
> considering the covalent bonds between them.
>
>
You may try PDBsum. On the ligand page for 1h4p
(NAG-NAG-BMA-BMA-MAN-BMA-MAN-MAN-BMA-BMA), you will find this file (link in
picture sphere above jmol logo) :
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/RunRomLas.pl?pdb=1h4p_02_01=pdbsum=YES=-l_atoms=YES

This file seems to contain the structure of the full ligand - but
unfortunately in PDB format, with some CONECT at least.

Otherwise, the cif file of 1h4p seems to contain all the needed information
too.
E.g. look for _pdbx_nonpoly_scheme.asym_id in
http://www.rcsb.org/pdb/files/1H4P.cif : the asym_id G is only for the
ligand NAG-NAG-BMA-BMA-MAN-BMA-MAN-MAN-BMA-BMA. Unfortunately, I'm not
familiar enough yet with the mmcif format for additional hint, but I think
you can get somehow the full ligand with the mmcif file.
But anyway you will need many fixes to get the correct ligands structure
for such tricky cases, as for the occupancy problem.

You could try the CCL list too for this question.

I hope it helps a bit :)

Regards,
Pascal
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