rdock-list-def — General Mailing List for rDock users

Re: [rDock-list-def] Segmentation fault (core dumped)

[pascal k. <pas...@un...>]

Hi,

My problem doesn't come from rDock but from my imput file.

I resolved it by using the following conversion with open babel.

obabel name.sdf -O name.mol2

obabel name.mol2 -O name.sdf

Pascal

On 11/27/2019 05:27 PM, pascal krezel wrote:
> Hi,
>
> rDock works well but I found a situation that creates a segmentation 
> fault.
>
> I give you a zip with all the files to reproduce the problem.
>
> It works with the original ligand "ligand.sdf" but it fails with 
> "mol.sdf".
>
> Where does the problem come from ?
>
> Pascal
>
>

[rDock-list-def] Platinum

[Rajat D. <raj...@gm...>]

Dear rDock developers,
I am a new rDock user, and wanted to know if the program supports small
molecules with Platinum and Boron? I would also like to see the list of all
supported atom types if available.

Thank you for your time!

Regards,
Rajat

Re: [rDock-list-def] Definition of pdb file for waters

[Markus M. <me...@gm...>]

Dear Pascal;
If I understand your question correctly have a look at the manual. There in
chapter 8.3 is the solvent definition section described.
You can define how you would like to treat your waters.
Best,
Markus

On Thu, Nov 7, 2019 at 9:06 AM pascal krezel <pas...@un...>
wrote:

> Hi,
>
> I have some problems with the definition of the pdb file for waters.
>
> If I want all free, how should I write it:
>
> HEADER HYDROLASE
> REMARK 99
> REMARK  99 MOE v2016.08 (Chemical Computing Group Inc.) Thu Nov  7
> 11:38:11 2019
> HETATM    1 OW HOH W   112   50.895   64.748   20.959 1.00 8.00
> HETATM    2 OW HOH W   113   45.384   40.342   22.069 1.00 8.00
> HETATM    3 OW HOH W   114   38.588   39.920    8.942 1.00 8.00
> HETATM    4 OW HOH W   115   41.945   60.472    9.691 1.00 8.00
> HETATM    5 OW HOH W   116   33.544   50.283    1.280 1.00 8.00
> HETATM    6 OW HOH W   117   45.986   60.872    3.752 1.00 8.00
> HETATM    7 OW HOH W   118   45.771   38.003   18.995 1.00 8.00
> END
>
> or
>
> HEADER HYDROLASE
> REMARK 99
> REMARK  99 MOE v2016.08 (Chemical Computing Group Inc.) Thu Nov  7
> 11:38:11 2019
> HETATM    1 OW HOH W   112   50.895   64.748   20.959 8.00 8.00
> HETATM    2 OW HOH W   113   45.384   40.342   22.069 8.00 8.00
> HETATM    3 OW HOH W   114   38.588   39.920    8.942 8.00 8.00
> HETATM    4 OW HOH W   115   41.945   60.472    9.691 8.00 8.00
> HETATM    5 OW HOH W   116   33.544   50.283    1.280 8.00 8.00
> HETATM    6 OW HOH W   117   45.986   60.872    3.752 8.00 8.00
> HETATM    7 OW HOH W   118   45.771   38.003   18.995 8.00 8.00
> END
>
> Sincerely.
>
> Pascal KREZEL
>
>
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] Definition of pdb file for waters

[pascal k. <pas...@un...>]

Hi,

I have some problems with the definition of the pdb file for waters.

If I want all free, how should I write it:

HEADER HYDROLASE
REMARK 99
REMARK  99 MOE v2016.08 (Chemical Computing Group Inc.) Thu Nov  7 
11:38:11 2019
HETATM    1 OW HOH W   112   50.895   64.748   20.959 1.00 8.00
HETATM    2 OW HOH W   113   45.384   40.342   22.069 1.00 8.00
HETATM    3 OW HOH W   114   38.588   39.920    8.942 1.00 8.00
HETATM    4 OW HOH W   115   41.945   60.472    9.691 1.00 8.00
HETATM    5 OW HOH W   116   33.544   50.283    1.280 1.00 8.00
HETATM    6 OW HOH W   117   45.986   60.872    3.752 1.00 8.00
HETATM    7 OW HOH W   118   45.771   38.003   18.995 1.00 8.00
END

or

HEADER HYDROLASE
REMARK 99
REMARK  99 MOE v2016.08 (Chemical Computing Group Inc.) Thu Nov  7 
11:38:11 2019
HETATM    1 OW HOH W   112   50.895   64.748   20.959 8.00 8.00
HETATM    2 OW HOH W   113   45.384   40.342   22.069 8.00 8.00
HETATM    3 OW HOH W   114   38.588   39.920    8.942 8.00 8.00
HETATM    4 OW HOH W   115   41.945   60.472    9.691 8.00 8.00
HETATM    5 OW HOH W   116   33.544   50.283    1.280 8.00 8.00
HETATM    6 OW HOH W   117   45.986   60.872    3.752 8.00 8.00
HETATM    7 OW HOH W   118   45.771   38.003   18.995 8.00 8.00
END

Sincerely.

Pascal KREZEL

Re: [rDock-list-def] rDock listo def

[Markus M. <me...@gm...>]

My apologies.
Wrong email list :-(
Markus

> On Nov 5, 2019, at 5:38 PM, Edgar Fernádez <edg...@gm...> wrote:
> 
> m

[rDock-list-def] rDock listo def

[Edgar F. <edg...@gm...>]

Hi!

there is in rDock program any option that allows me to assingn flexible
aminoacids?
Thanks!

El mar., 5 de noviembre de 2019 6:52 p. m., Markus Metz <me...@gm...>
escribió:

> Hello all:
> I just came across the description of this package on rdkit.org.
> However, it seems there is not much to import.
> When I type
> from rdkit.ML.Scoring import 'tab'
> I am getting
> Scoring
> __doc__
> __file__
> __name__
> __package__
> Can you please clarify?
> I am using rdkit.2019.09.1.
> Many thanks in advance,
> Markus
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] rdkit.ML.Scoring package?

[Markus M. <me...@gm...>]

Hello all:
I just came across the description of this package on rdkit.org.
However, it seems there is not much to import.
When I type
from rdkit.ML.Scoring import 'tab'
I am getting
Scoring
__doc__
__file__
__name__
__package__
Can you please clarify?
I am using rdkit.2019.09.1.
Many thanks in advance,
Markus

Re: [rDock-list-def] rdock and the SDF property issue

[Peter S. <pet...@gm...>]

Hey, cool and thanks looking into this. It’s a bit the same for me, would be good to know more about that. 

In the two file you sent, 

the one written with Pipeline Pilot has a less extensive description of the atoms and bond order first of all, but also has different header descriptions. 
The one written with knime all fields of the mol file in v2000 are specified. 
For the descriptor part (Index) I guess both are the same even though you might want to check the newlines at the end (but I already did that in the past and it wasn’t the issue in my case). 

So I’d start to permutate a bit between both files to narrow down it’s the header / atom or bond section messing things up here. 

Cannot do this right now on my own here, but maybe some time next week.

Thanks for looking into this anyway.



Peter

> On 24 Oct 2019, at 20:32, Scott Bembenek <sbe...@de...> wrote:
> 
> Hi Peter,
> 
> Sorry to mail you directly, I am unclear what email to send it to so that it post on the forum. 
> 
> Question, that has been on mind for awhile ... 
> 
> The problem with including properties in the input SDF has been discussed. I have also run into this problem, but find that sometimes it happens and sometimes it does not. 
> 
> Doe anyone have any more insight into this? 
> 
> Here's an example where to two files written by different programs have the same properties in them, but one of them runs fine with rdock (format 2), while the other does not (format 1).
> 
> I'd be grateful if you have insight into the nature of "the property problem" since I find it is not consistent and also, it is often times nice/necessary to include at least one property in your input SDF. 
> 
> thanks! 
> 
> Scott
> <mol1_pp_format_index_format1.sdf><mol1_knime_format_index_format2.sdf>

[rDock-list-def] problem with nitro and azide groups

[Tim D. <tdu...@gm...>]

I'm finding that the rbdock program has problems with molecules 
containing nitro or azide groups. The molecules that are passed in have 
the correct charges but the poses that rbdock writes out seem to be 
missing the charges so are invalid.

Is this a known problem? I can provide more details if necessary.

Thanks
Tim

Re: [rDock-list-def] mol2 format

[Peter S. <pet...@gm...>]

Oh I didn’t even check the SD file. Indeed I also had issues with properties in the SD file if they are formatted in a particular way.
Easiest -> drop them if possible ;)

++

Peter

> On 24 Sep 2019, at 20:41, Markus Metz <me...@gm...> wrote:
> 
> Hello again:
> So I can confirm that the property fields in my sd file where the culprits.
> Thank you to everybody chiming in!!
> Best,
> Markus
> 
> On Tue, Sep 24, 2019 at 10:18 AM Peter Schmidtke <pet...@gm... <mailto:pet...@gm...>> wrote:
> Thanks Markus,
> 
> I got lost with the Markus’s here :) 
> 
> 
> 
>> On 23 Sep 2019, at 20:21, Markus Heller <mh...@ad... <mailto:mh...@ad...>> wrote:
>> 
>> Hi Markus,
>>  
>> I typically use UCSF’s Dock Prep tool.  Usually works pretty well.
>>  
>> Are you able to share an example of a protein file that fails?
>>  
>> Markus
>>  
>> From: Markus Metz <me...@gm... <mailto:me...@gm...>> 
>> Sent: Friday, September 20, 2019 4:01 PM
>> To: rdo...@li... <mailto:rdo...@li...>
>> Subject: [rDock-list-def] mol2 format
>>  
>> Hello all:
>> I am trying to convert my protein to mol2 format and I have tried the following:
>> a) converted via maestro 
>> b) used openbabel
>> c) used chimera  
>> d) visually tried to pinpoint where my mol2 file differs from tutorial examples.
>>  
>> In every case I failed to run the rbcavity command.
>> The best error message I am getting is
>> 'Corrupted MOL2 file: not enough fields in SUBSTRUCTURE'.
>>  
>> I can find no difference between the tutorial example and the mol2 file created.
>> Of course rbcavity works with the tutorial files.
>>  
>> How are you performing the mol2 conversion?
>> Kindly let me know,
>> Markus 
>> _______________________________________________
>> rDock-list-def mailing list
>> rDo...@li... <mailto:rDo...@li...>
>> https://lists.sourceforge.net/lists/listinfo/rdock-list-def <https://lists.sourceforge.net/lists/listinfo/rdock-list-def>

Re: [rDock-list-def] mol2 format

[Markus M. <me...@gm...>]

Hello again:
So I can confirm that the property fields in my sd file where the culprits.
Thank you to everybody chiming in!!
Best,
Markus

On Tue, Sep 24, 2019 at 10:18 AM Peter Schmidtke <pet...@gm...>
wrote:

> Thanks Markus,
>
> I got lost with the Markus’s here :)
>
>
>
> On 23 Sep 2019, at 20:21, Markus Heller <mh...@ad...> wrote:
>
> Hi Markus,
>
> I typically use UCSF’s Dock Prep tool.  Usually works pretty well.
>
> Are you able to share an example of a protein file that fails?
>
> Markus
>
> *From:* Markus Metz <me...@gm...>
> *Sent:* Friday, September 20, 2019 4:01 PM
> *To:* rdo...@li...
> *Subject:* [rDock-list-def] mol2 format
>
> Hello all:
> I am trying to convert my protein to mol2 format and I have tried the
> following:
> a) converted via maestro
> b) used openbabel
> c) used chimera
> d) visually tried to pinpoint where my mol2 file differs from tutorial
> examples.
>
> In every case I failed to run the rbcavity command.
> The best error message I am getting is
> 'Corrupted MOL2 file: not enough fields in SUBSTRUCTURE'.
>
> I can find no difference between the tutorial example and the mol2 file
> created.
> Of course rbcavity works with the tutorial files.
>
> How are you performing the mol2 conversion?
> Kindly let me know,
> Markus
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>
>
>

Re: [rDock-list-def] mol2 format

[Peter S. <pet...@gm...>]

Thanks Markus,

I got lost with the Markus’s here :) 



> On 23 Sep 2019, at 20:21, Markus Heller <mh...@ad...> wrote:
> 
> Hi Markus,
>  
> I typically use UCSF’s Dock Prep tool.  Usually works pretty well.
>  
> Are you able to share an example of a protein file that fails?
>  
> Markus
>  
> From: Markus Metz <me...@gm... <mailto:me...@gm...>> 
> Sent: Friday, September 20, 2019 4:01 PM
> To: rdo...@li... <mailto:rdo...@li...>
> Subject: [rDock-list-def] mol2 format
>  
> Hello all:
> I am trying to convert my protein to mol2 format and I have tried the following:
> a) converted via maestro 
> b) used openbabel
> c) used chimera  
> d) visually tried to pinpoint where my mol2 file differs from tutorial examples.
>  
> In every case I failed to run the rbcavity command.
> The best error message I am getting is
> 'Corrupted MOL2 file: not enough fields in SUBSTRUCTURE'.
>  
> I can find no difference between the tutorial example and the mol2 file created.
> Of course rbcavity works with the tutorial files.
>  
> How are you performing the mol2 conversion?
> Kindly let me know,
> Markus 
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li... <mailto:rDo...@li...>
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def <https://lists.sourceforge.net/lists/listinfo/rdock-list-def>

Re: [rDock-list-def] mol2 format

[Markus M. <me...@gm...>]

Thanks Peter:
Actually I think I found the issue.
Could you please do me a favor and go into the ligand sd file and remove
all property fields and try rerunning the cavity calculation?
Thank you so much for your time!
Markus

On Tue, Sep 24, 2019 at 9:53 AM Peter Schmidtke <pet...@gm...>
wrote:

> I personally get a Segfault with your input files. Probably yet another
> problem for now.
> On 3decision.discngine.cloud we use rdock behind the scenes and rbcavity
> runs fine.
>
> There we use pdb2pqr + open babel . I attach the sample mol2 that works
> over here.
>
> I suspect your section :
>
> 1 ALA1B  to mess things up maybe?
>
> I don’t have maestro, so cannot check that out in detail, but I suspect
> the mol2 format is not standard.
>
> Could you try to drop all alternates, unnecessary chains etc to test this?
>
> Peter
>
>
>
> On 24 Sep 2019, at 17:38, Markus Metz <me...@gm...> wrote:
>
> Dear Markus and Peter:
> Apologies for the delay!
>
> Here is an example:
> I downloaded 1oyt for rcsb.org and processed it within maestro using the
> prep wizard.
> And the ligand is also attached. I exported this ligand in mol format from
> maestro and converted it via obabel to sdf.
>
> According to the manual rdock reads the atom name, cart cords and tripos
> atom types. So all the other info is discarded?
> Otherwise may be the numbering of the residues in the ATOM section is
> different.
>
> Best,
> Markus
>
> On Tue, Sep 24, 2019 at 8:26 AM Peter Schmidtke <pet...@gm...>
> wrote:
>
>> Hey Markus,
>>
>> any chance you can share the faulty mol2 files?
>> I personally use open babel to do that.
>>
>> ++
>>
>> Peter
>>
>> > On 21 Sep 2019, at 01:00, Markus Metz <me...@gm...> wrote:
>> >
>> > Hello all:
>> > I am trying to convert my protein to mol2 format and I have tried the
>> following:
>> > a) converted via maestro
>> > b) used openbabel
>> > c) used chimera
>> > d) visually tried to pinpoint where my mol2 file differs from tutorial
>> examples.
>> >
>> > In every case I failed to run the rbcavity command.
>> > The best error message I am getting is
>> > 'Corrupted MOL2 file: not enough fields in SUBSTRUCTURE'.
>> >
>> > I can find no difference between the tutorial example and the mol2 file
>> created.
>> > Of course rbcavity works with the tutorial files.
>> >
>> > How are you performing the mol2 conversion?
>> > Kindly let me know,
>> > Markus
>> > _______________________________________________
>> > rDock-list-def mailing list
>> > rDo...@li...
>> > https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>>
>> <1oyt_min_prot.mol2><1oyt_min_lig.sd>
>
>
>

Re: [rDock-list-def] mol2 format

[Peter S. <pet...@gm...>]

I personally get a Segfault with your input files. Probably yet another problem for now. 

On 3decision.discngine.cloud we use rdock behind the scenes and rbcavity runs fine. 

There we use pdb2pqr + open babel . I attach the sample mol2 that works over here. 

I suspect your section : 

1 ALA1B  to mess things up maybe?

I don’t have maestro, so cannot check that out in detail, but I suspect the mol2 format is not standard. 

Could you try to drop all alternates, unnecessary chains etc to test this?

Peter



> On 24 Sep 2019, at 17:38, Markus Metz <me...@gm...> wrote:
> 
> Dear Markus and Peter:
> Apologies for the delay!
> 
> Here is an example:
> I downloaded 1oyt for rcsb.org <http://rcsb.org/> and processed it within maestro using the prep wizard.
> And the ligand is also attached. I exported this ligand in mol format from maestro and converted it via obabel to sdf.
>  
> According to the manual rdock reads the atom name, cart cords and tripos atom types. So all the other info is discarded?
> Otherwise may be the numbering of the residues in the ATOM section is different.
> 
> Best,
> Markus
> 
> On Tue, Sep 24, 2019 at 8:26 AM Peter Schmidtke <pet...@gm... <mailto:pet...@gm...>> wrote:
> Hey Markus,
> 
> any chance you can share the faulty mol2 files?
> I personally use open babel to do that.
> 
> ++
> 
> Peter
> 
> > On 21 Sep 2019, at 01:00, Markus Metz <me...@gm... <mailto:me...@gm...>> wrote:
> > 
> > Hello all:
> > I am trying to convert my protein to mol2 format and I have tried the following:
> > a) converted via maestro 
> > b) used openbabel
> > c) used chimera  
> > d) visually tried to pinpoint where my mol2 file differs from tutorial examples.
> > 
> > In every case I failed to run the rbcavity command.
> > The best error message I am getting is
> > 'Corrupted MOL2 file: not enough fields in SUBSTRUCTURE'.
> > 
> > I can find no difference between the tutorial example and the mol2 file created.
> > Of course rbcavity works with the tutorial files.
> > 
> > How are you performing the mol2 conversion?
> > Kindly let me know,
> > Markus 
> > _______________________________________________
> > rDock-list-def mailing list
> > rDo...@li... <mailto:rDo...@li...>
> > https://lists.sourceforge.net/lists/listinfo/rdock-list-def <https://lists.sourceforge.net/lists/listinfo/rdock-list-def>
> 
> <1oyt_min_prot.mol2><1oyt_min_lig.sd>

Re: [rDock-list-def] mol2 format

[Markus M. <me...@gm...>]

Dear Markus and Peter:
Apologies for the delay!

Here is an example:
I downloaded 1oyt for rcsb.org and processed it within maestro using the
prep wizard.
And the ligand is also attached. I exported this ligand in mol format from
maestro and converted it via obabel to sdf.

According to the manual rdock reads the atom name, cart cords and tripos
atom types. So all the other info is discarded?
Otherwise may be the numbering of the residues in the ATOM section is
different.

Best,
Markus

On Tue, Sep 24, 2019 at 8:26 AM Peter Schmidtke <pet...@gm...>
wrote:

> Hey Markus,
>
> any chance you can share the faulty mol2 files?
> I personally use open babel to do that.
>
> ++
>
> Peter
>
> > On 21 Sep 2019, at 01:00, Markus Metz <me...@gm...> wrote:
> >
> > Hello all:
> > I am trying to convert my protein to mol2 format and I have tried the
> following:
> > a) converted via maestro
> > b) used openbabel
> > c) used chimera
> > d) visually tried to pinpoint where my mol2 file differs from tutorial
> examples.
> >
> > In every case I failed to run the rbcavity command.
> > The best error message I am getting is
> > 'Corrupted MOL2 file: not enough fields in SUBSTRUCTURE'.
> >
> > I can find no difference between the tutorial example and the mol2 file
> created.
> > Of course rbcavity works with the tutorial files.
> >
> > How are you performing the mol2 conversion?
> > Kindly let me know,
> > Markus
> > _______________________________________________
> > rDock-list-def mailing list
> > rDo...@li...
> > https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>
>

Re: [rDock-list-def] mol2 format

[Peter S. <pet...@gm...>]

Hey Markus,

any chance you can share the faulty mol2 files?
I personally use open babel to do that.

++

Peter

> On 21 Sep 2019, at 01:00, Markus Metz <me...@gm...> wrote:
> 
> Hello all:
> I am trying to convert my protein to mol2 format and I have tried the following:
> a) converted via maestro 
> b) used openbabel
> c) used chimera  
> d) visually tried to pinpoint where my mol2 file differs from tutorial examples.
> 
> In every case I failed to run the rbcavity command.
> The best error message I am getting is
> 'Corrupted MOL2 file: not enough fields in SUBSTRUCTURE'.
> 
> I can find no difference between the tutorial example and the mol2 file created.
> Of course rbcavity works with the tutorial files.
> 
> How are you performing the mol2 conversion?
> Kindly let me know,
> Markus 
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def

Re: [rDock-list-def] mol2 format

[Markus H. <mh...@ad...>]

Hi Markus,

I typically use UCSF’s Dock Prep tool.  Usually works pretty well.

Are you able to share an example of a protein file that fails?

Markus

From: Markus Metz <me...@gm...>
Sent: Friday, September 20, 2019 4:01 PM
To: rdo...@li...
Subject: [rDock-list-def] mol2 format

Hello all:
I am trying to convert my protein to mol2 format and I have tried the following:
a) converted via maestro
b) used openbabel
c) used chimera
d) visually tried to pinpoint where my mol2 file differs from tutorial examples.

In every case I failed to run the rbcavity command.
The best error message I am getting is
'Corrupted MOL2 file: not enough fields in SUBSTRUCTURE'.

I can find no difference between the tutorial example and the mol2 file created.
Of course rbcavity works with the tutorial files.

How are you performing the mol2 conversion?
Kindly let me know,
Markus

[rDock-list-def] mol2 format

[Markus M. <me...@gm...>]

Hello all:
I am trying to convert my protein to mol2 format and I have tried the
following:
a) converted via maestro
b) used openbabel
c) used chimera
d) visually tried to pinpoint where my mol2 file differs from tutorial
examples.

In every case I failed to run the rbcavity command.
The best error message I am getting is
'Corrupted MOL2 file: not enough fields in SUBSTRUCTURE'.

I can find no difference between the tutorial example and the mol2 file
created.
Of course rbcavity works with the tutorial files.

How are you performing the mol2 conversion?
Kindly let me know,
Markus

Re: [rDock-list-def] Problem with installation

[Markus H. <mh...@cd...>]

As outlined by Peter, try a Docker image from here: https://hub.docker.com/r/informaticsmatters/rdock/https://hub.docker.com/r/informaticsmatters/rdock/

Peter's post from Nov 22, 2018 for your reference:

Hi all,

sorry for the inactivity of the mailing list lately;
Regarding all compilation issues with rdock. Things can get tricky especially with always changing compilers and moving shared libraries in all distributions. We cannot keep track and test all of these, so if possible I recommend to use a docker image of rdock :
https://hub.docker.com/r/informaticsmatters/rdock/

It’s not an option if you want to modify the source code yourself, but it’s definitely a good one if you just want to use the program without the huzzle of the installation / compilation procedure.

Best regards

Peter
________________________________
From: KYEONG MO KIM via rDock-list-def [rdo...@li...]
Sent: Thursday, February 28, 2019 9:41 AM
To: rdo...@li...
Subject: [rDock-list-def] Problem with installation

Hi!

I was trying to install rDOCK, but this error came up

/usr/include/c++/4.8.2/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
 #error This file requires compiler and library support for the \

How should I fix this?

[rDock-list-def] Problem with installation

[KYEONG MO K. <kk...@wi...>]

Hi!

I was trying to install rDOCK, but this error came up

/usr/include/c++/4.8.2/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
 #error This file requires compiler and library support for the \

How should I fix this?

[rDock-list-def] compilation issues with rdock

[Peter S. <pet...@gm...>]

Hi all,

sorry for the inactivity of the mailing list lately; 
Regarding all compilation issues with rdock. Things can get tricky especially with always changing compilers and moving shared libraries in all distributions. We cannot keep track and test all of these, so if possible I recommend to use a docker image of rdock : 
https://hub.docker.com/r/informaticsmatters/rdock/ <https://hub.docker.com/r/informaticsmatters/rdock/>

It’s not an option if you want to modify the source code yourself, but it’s definitely a good one if you just want to use the program without the huzzle of the installation / compilation procedure.

Best regards

Peter

[rDock-list-def] How to increase the number of poses ?

[pascal k. <pas...@un...>]

Hi,

I need to increase the number of poses found by rDock. It seems to be 
limited to 1000.

How can I do that ?

Sincerely.

Pascal

[rDock-list-def] Compilation fails

[Markus H. <mh...@cd...>]

Hi,

I'm trying to compile rdock under Ubuntu 16.04.2 LTS, and get the following error (just a snippet; entire log is too long):

make[2]: Leaving directory '/home/mheller/Downloads/rdock-git/build'
make -j 4		 -f Makefile.linux-g++-64-release-exe unit_test
make[2]: Entering directory '/home/mheller/Downloads/rdock-git/build'
/usr/bin/g++ -pipe -m64 -fpermissive  -Wno-deprecated -fPIC -O3 -ffast-math  -D_NDEBUG -I../include -I../include/GP -Llinux-g++-64/release/lib -I./test ./test/*.cxx -lRbt -ldl -lcppunit -o ./test/unit_test
In file included from ../include/RbtPolarIdxSF.h:21:0,
                 from ./test/OccupancyTest.cxx:7:
../include/RbtPolarSF.h:81:5: warning: extra qualification ‘RbtPolarSF::f1prms::’ on member ‘f1prms’ [-fpermissive]
     f1prms::f1prms(RbtDouble R, RbtDouble DMin, RbtDouble DMax)
     ^
make[2]: Leaving directory '/home/mheller/Downloads/rdock-git/build'
cp -df linux-g++-64/release/exe/* ../bin	
make[1]: Leaving directory '/home/mheller/Downloads/rdock-git/build'
% 


This is under csh. As far as dependencies go: g++ and gcc are 4:5.3.1; make is 4.1-6.

I can't find popt or popt-devel using apt, but I installed libpopt0 (1.16-10) and libpopt-dev (1.16-10), which are the replacements suggested by apt.  Similar for cppunit and cppunit-devel: apt can't find them and I ninstalled the recommendations: libcppunit-dev (1.13.2-2.1).

How do I fix this and get the compilation to complete?

Thanks
Markus

[rDock-list-def] rDock scoring function

[Luba S. <lub...@gm...>]

Hello,

I'm a new user of rDock software.
I would like to know what is the standard deviation of the scores of
different poses, i.e. which difference between scoring values would be
considered as significant?

Thanks,
Luba

[rDock-list-def] Compilation issue

[pgrzeskowiak <pgr...@ch...>]

Hi,

I am having exact same issues as @Ivan, compiler spits out multiple errors( to long to post here) and finishes with similar output as Ivan’s.

Is this a legacy issue?
I am running Fedora 26 64bit, and I’ve double checked all dependancies.

Best

Piotr