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

Re: [rDock-list-def] Failure to handle charges in ligands

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

Tim:
Please check out the rdkit user list.
Andrew Dahlke provided also a python script to overcome this issue.
best,
Markus

> On Oct 8, 2020, at 10:19 AM, Tim Dudgeon <tdu...@gm...> wrote:
> 
> Ah, thanks. That's good to know.
> I'm using RDKit that adds the info as CHG lines and not to the atom lines as that is the "correct" way to do it now.
> Tim 
> 
> On Thu, Oct 8, 2020 at 6:11 PM Markus Metz <me...@gm... <mailto:me...@gm...>> wrote:
> Hi Tim:
> I know you did not ask this.
> But for reference:
> If you use for example openbabel the column charges are added and all works fine.
> Markus
> 
> 
>> On Oct 8, 2020, at 9:33 AM, Tim Dudgeon <tdu...@gm... <mailto:tdu...@gm...>> wrote:
>> 
>> This was raised a long time ago, but the problem seems to remain:
>> https://sourceforge.net/p/rdock/mailman/message/34741112/ <https://sourceforge.net/p/rdock/mailman/message/34741112/>
>> 
>> rDock is not respecting the CHG lines in the molblock section.
>> It reports out messages like:
>> **WARNING** RBT_MODEL_ERROR at ../src/lib/RbtMdlFileSource.cxx, line 413
>> N13 makes too many bonds
>> 
>> The SDF it writes out is missing the charge information and so the molecule is not correct.
>> Presumably, also, if the charges are missing then the energetics of the docking scoring must be badly wrong?
>> 
>> Are there plans to address this?
>> _______________________________________________
>> 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] Failure to handle charges in ligands

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

Ah, thanks. That's good to know.
I'm using RDKit that adds the info as CHG lines and not to the atom lines
as that is the "correct" way to do it now.
Tim

On Thu, Oct 8, 2020 at 6:11 PM Markus Metz <me...@gm...> wrote:

> Hi Tim:
> I know you did not ask this.
> But for reference:
> If you use for example openbabel the column charges are added and all
> works fine.
> Markus
>
>
> On Oct 8, 2020, at 9:33 AM, Tim Dudgeon <tdu...@gm...> wrote:
>
> This was raised a long time ago, but the problem seems to remain:
> https://sourceforge.net/p/rdock/mailman/message/34741112/
>
> rDock is not respecting the CHG lines in the molblock section.
> It reports out messages like:
> **WARNING** RBT_MODEL_ERROR at ../src/lib/RbtMdlFileSource.cxx, line 413
> N13 makes too many bonds
>
> The SDF it writes out is missing the charge information and so the
> molecule is not correct.
> Presumably, also, if the charges are missing then the energetics of the
> docking scoring must be badly wrong?
>
> Are there plans to address this?
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>
>
>

Re: [rDock-list-def] Failure to handle charges in ligands

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

Hi Tim:
I know you did not ask this.
But for reference:
If you use for example openbabel the column charges are added and all works fine.
Markus


> On Oct 8, 2020, at 9:33 AM, Tim Dudgeon <tdu...@gm...> wrote:
> 
> This was raised a long time ago, but the problem seems to remain:
> https://sourceforge.net/p/rdock/mailman/message/34741112/ <https://sourceforge.net/p/rdock/mailman/message/34741112/>
> 
> rDock is not respecting the CHG lines in the molblock section.
> It reports out messages like:
> **WARNING** RBT_MODEL_ERROR at ../src/lib/RbtMdlFileSource.cxx, line 413
> N13 makes too many bonds
> 
> The SDF it writes out is missing the charge information and so the molecule is not correct.
> Presumably, also, if the charges are missing then the energetics of the docking scoring must be badly wrong?
> 
> Are there plans to address this?
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def

[rDock-list-def] Failure to handle charges in ligands

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

This was raised a long time ago, but the problem seems to remain:
https://sourceforge.net/p/rdock/mailman/message/34741112/

rDock is not respecting the CHG lines in the molblock section.
It reports out messages like:
**WARNING** RBT_MODEL_ERROR at ../src/lib/RbtMdlFileSource.cxx, line 413
N13 makes too many bonds

The SDF it writes out is missing the charge information and so the molecule
is not correct.
Presumably, also, if the charges are missing then the energetics of the
docking scoring must be badly wrong?

Are there plans to address this?

[rDock-list-def] Restart of rDock runs

[Tatikonda, R. R. <rta...@ut...>]

Dear Team,

I am using rDock for docking small molecules to RNA. My docking jobs got aborted due to time-limit. I would like to know if there is a way that I can restart my docking runs.

Your help is appreciated.

Thanks in advance,
Rajitha

Re: [rDock-list-def] How to run rdock from python script?

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

Hi,

you probably don’t have all required environment variables defined when running through subprocess.run You should make sure of that. 

Else consider also using rdock through docker, makes some of the install / usage things much easier.

Peter



> On 2 Sep 2020, at 13:25, Studia Studia <stu...@gm...> wrote:
> 
> Hello! Is it possible to run rDock from a python script? How can this be done? I tried subprocess.run () but it doesn't work.
> 
> M.
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def

[rDock-list-def] How to run rdock from python script?

[Studia S. <stu...@gm...>]

Hello! Is it possible to run rDock from a python script? How can this be
done? I tried subprocess.run () but it doesn't work.

M.

[rDock-list-def] Can I change the docking algorithm?

[Studia S. <stu...@gm...>]

Hello, I would like to ask if I can change the docking algorithm contained
in the file dock.prm by for example excluding the Monte Carlo algorithm?


Meg

Re: [rDock-list-def] tethered docking question

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

Hello again:
I feel I should reply here to close this case:
After some thorough checking I realized that I had typo.
So all works now as expected.
Best,
Markus

> On Jul 6, 2020, at 3:57 PM, Markus Metz <me...@gm...> wrote:
> 
> Hello all:
> 
> I am interested to conduct some tethered docking experiments with rDock and I found Peter’s blog about tethered docking in rDock:
> https://www.discngine.com/blog/2019/6/6/tethered-minimization-of-small-molecules-with-rdkit-towards-tethered-docking-on-proteins-with-rdock <https://www.discngine.com/blog/2019/6/6/tethered-minimization-of-small-molecules-with-rdkit-towards-tethered-docking-on-proteins-with-rdock>
> 
> So, with this I know how to conduct the tethered docking.
> However, I have some issues to understand what to expect from these calculations.
> No matter what tethering options I choose (options taken form Tim’s question linked below) all of my docking results shift quite a bit relative to my core.
> 
> I found a question regarding tethered docking was asked recently by Tim:
> https://sourceforge.net/p/rdock/mailman/rdock-list-def/thread/f51ced34-6fe8-204d-64e3-49703afdfc9a%40gmail.com/#msg36997946 <https://sourceforge.net/p/rdock/mailman/rdock-list-def/thread/f51...@gm.../#msg36997946>
> But it does not exactly answer my question.
> 
> My questions is: 
> Is it possible to enforce the coordinates of my template on my compounds with tethered docking and remove those docking poses which have some steric clashes with the binding site residues?
> 
> Best,
> Markus

[rDock-list-def] tethered docking question

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

Hello all:

I am interested to conduct some tethered docking experiments with rDock and I found Peter’s blog about tethered docking in rDock:
https://www.discngine.com/blog/2019/6/6/tethered-minimization-of-small-molecules-with-rdkit-towards-tethered-docking-on-proteins-with-rdock <https://www.discngine.com/blog/2019/6/6/tethered-minimization-of-small-molecules-with-rdkit-towards-tethered-docking-on-proteins-with-rdock>

So, with this I know how to conduct the tethered docking.
However, I have some issues to understand what to expect from these calculations.
No matter what tethering options I choose (options taken form Tim’s question linked below) all of my docking results shift quite a bit relative to my core.

I found a question regarding tethered docking was asked recently by Tim:
https://sourceforge.net/p/rdock/mailman/rdock-list-def/thread/f51ced34-6fe8-204d-64e3-49703afdfc9a%40gmail.com/#msg36997946 <https://sourceforge.net/p/rdock/mailman/rdock-list-def/thread/f51...@gm.../#msg36997946>
But it does not exactly answer my question.

My questions is: 
Is it possible to enforce the coordinates of my template on my compounds with tethered docking and remove those docking poses which have some steric clashes with the binding site residues?

Best,
Markus

[rDock-list-def] rDock, checkpointing & AWS spot instances

[Scott B. <sbe...@de...>]

I am wondering how people are dealing with checkpointing for rDock. My
workaround is to look in the output file I write to determine where the job
left off (when it died or was killed) and then write a new input file.

Ideally, one wants to start rDock from the particular point (it left off)
in the existing input file. It's on my mind, since this is important for
using spot instances on AWS since they come and go at will, forcing rDock
to start over from the beginning.

thanks,

Scott

[rDock-list-def] NMR Restrains in

[Ridvan N. <rin...@gm...>]

Hello
I am interested in your NMR restrains such as NoE implementation within
rDock ....
In your Ruis-Carmona S. et al  2014
<https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003571>
paper  paper you anticipate that: citing from your paper "When experimental
NMR distance limits (NOE or STD) are known for a specific ligand,
restraints can be used to ensure that a minimum distance is fulfilled
between an atom (or group of atoms) of the ligand and an atom (or group of
atoms) of the receptorNMR NOE restrains are also possible " .....but I
didn't find anything in the manual...
Is there a way on how to implement them in your software
Thank you in advance for any possible explanation
All the best
Ridvan

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

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

Hello,

this can happen for various reasons. Can you share your input files and run rbdock with debugging on (trace level set to something high)

Cheers

Peter

> On 7 May 2020, at 22:01, Studia Studia <stu...@gm...> wrote:
> 
> Hello!
> 
> I'm trying to dock with rdock but after using the rbdock command I get the following error: segmentation fault (core dumped).
> 
> I have Ubuntu 16.04 installed on the virtual machine for the parameters:
> 
> RAM 3MB
> Memory 10GB and 1CPU
> 
> Is the error due to insufficient memory? What should the parameters be for everything to work?
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def

[rDock-list-def] segmentation fault (core dumped) error

[Studia S. <stu...@gm...>]

Hello!

I'm trying to dock with rdock but after using the rbdock command I get the
following error: segmentation fault (core dumped).

I have Ubuntu 16.04 installed on the virtual machine for the parameters:

RAM 3MB
Memory 10GB and 1CPU

Is the error due to insufficient memory? What should the parameters be for
everything to work?

Re: [rDock-list-def] Tethering params

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

Hi Peter,

yes, some definitely will be generating clashes. That's really the point 
of this - to be able to quickly filter those out.

Tim

On 30/04/2020 22:28, Peter Schmidtke wrote:
> Hi Tim,
>
> are you docking compounds that generate important clashes when they 
> are tethered?
>
> usually the MAX_TRANS and MAX_ROT parameters respond fairly well. We 
> use for instance 0.1 & 0.1 for both often.
>
> Peter
>
>
>
>> On 30 Apr 2020, at 16:41, Tim Dudgeon <tdu...@gm... 
>> <mailto:tdu...@gm...>> wrote:
>>
>> I'd like a clarification on the use of tethering parameters (the 
>> LIGAND section of the configuration file).
>>
>> I started by using the default parameters that seem to be recommended:
>>
>> SECTION LIGAND
>>      TRANS_MODE TETHERED
>>      ROT_MODE TETHERED
>>      DIHEDRAL_MODE FREE
>>      MAX_TRANS 1
>>      MAX_ROT 30
>> END_SECTION
>>
>> The results show that the poses are tethered but the tethering is 
>> relatively weak. So I tightened up the params to this
>>
>> SECTION LIGAND
>>      TRANS_MODE TETHERED
>>      ROT_MODE TETHERED
>>      DIHEDRAL_MODE FREE
>>      MAX_TRANS 0.2
>>      MAX_ROT 5
>> END_SECTION
>>
>> But this had very minimal impact. The poses we still fairly weakly 
>> tethered. I would have expected the pose to be pretty well anchored 
>> to the position of the tethered atoms.
>>
>> Finally I tried FIXING the positions using:
>>
>> SECTION LIGAND
>>      TRANS_MODE FIXED
>>      ROT_MODE FIXED
>>      DIHEDRAL_MODE FREE
>> END_SECTION
>>
>> Not sure if this is supported. I was hoping that it fixes the 
>> tethered atoms but allows the other ones to move. But what happened 
>> is that some of the tethered atom were pretty well fixed, but others 
>> moved widely.
>>
>> Can someone explain?
>>
>> Thanks
>> Tim
>>
>>
>>
>> _______________________________________________
>> rDock-list-def mailing list
>> rDo...@li... 
>> <mailto:rDo...@li...>
>> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

Re: [rDock-list-def] Tethering params

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

Hi Tim,

are you docking compounds that generate important clashes when they are tethered? 

usually the MAX_TRANS and MAX_ROT parameters respond fairly well. We use for instance 0.1 & 0.1 for both often. 

Peter



> On 30 Apr 2020, at 16:41, Tim Dudgeon <tdu...@gm...> wrote:
> 
> I'd like a clarification on the use of tethering parameters (the LIGAND section of the configuration file).
> 
> I started by using the default parameters that seem to be recommended:
> 
> SECTION LIGAND
>     TRANS_MODE TETHERED
>     ROT_MODE TETHERED
>     DIHEDRAL_MODE FREE
>     MAX_TRANS 1
>     MAX_ROT 30
> END_SECTION
> 
> The results show that the poses are tethered but the tethering is relatively weak. So I tightened up the params to this
> 
> SECTION LIGAND
>     TRANS_MODE TETHERED
>     ROT_MODE TETHERED
>     DIHEDRAL_MODE FREE
>     MAX_TRANS 0.2
>     MAX_ROT 5
> END_SECTION
> But this had very minimal impact. The poses we still fairly weakly tethered. I would have expected the pose to be pretty well anchored to the position of the tethered atoms.
> 
> Finally I tried FIXING the positions using:
> 
> SECTION LIGAND
>     TRANS_MODE FIXED
>     ROT_MODE FIXED
>     DIHEDRAL_MODE FREE
> END_SECTION
> Not sure if this is supported. I was hoping that it fixes the tethered atoms but allows the other ones to move. But what happened is that some of the tethered atom were pretty well fixed, but others moved widely.
> 
> Can someone explain?
> 
> Thanks
> Tim
> 
> 
> 
> 
> 
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def

[rDock-list-def] Tethering params

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

I'd like a clarification on the use of tethering parameters (the LIGAND 
section of the configuration file).

I started by using the default parameters that seem to be recommended:

SECTION LIGAND
     TRANS_MODE TETHERED
     ROT_MODE TETHERED
     DIHEDRAL_MODE FREE
     MAX_TRANS 1
     MAX_ROT 30
END_SECTION

The results show that the poses are tethered but the tethering is 
relatively weak. So I tightened up the params to this

SECTION LIGAND
     TRANS_MODE TETHERED
     ROT_MODE TETHERED
     DIHEDRAL_MODE FREE
     MAX_TRANS 0.2
     MAX_ROT 5
END_SECTION

But this had very minimal impact. The poses we still fairly weakly 
tethered. I would have expected the pose to be pretty well anchored to 
the position of the tethered atoms.

Finally I tried FIXING the positions using:

SECTION LIGAND
     TRANS_MODE FIXED
     ROT_MODE FIXED
     DIHEDRAL_MODE FREE
END_SECTION

Not sure if this is supported. I was hoping that it fixes the tethered 
atoms but allows the other ones to move. But what happened is that some 
of the tethered atom were pretty well fixed, but others moved widely.

Can someone explain?

Thanks
Tim

[rDock-list-def] Rdock gui installation problem

[samihamdoun <sam...@gm...>]

Hi,I tried to install the rdock gui. But it always gives an error when I run the makefiles.Any advice?Many thanks,Sami

Re: [rDock-list-def] How can I install rDock on Ubuntu 18.04?

[Munesh C. <mun...@gm...>]

Hi,
I could not figure out the installation for Ubuntu 18.04 after quite a few
tries.
But rdock definitely works on Ubuntu 16.04.

Munesh

On Sun 29 Mar, 2020, 2:51 AM Studia Studia, <stu...@gm...> wrote:

> Hello, I am a  begginer Ubuntu user -  I just installed Ubuntu 18.04 on a
> virtual machine because I need a rdock for my master's thesis.
>
> I tried to install rDock as per the instructions on the official website
> but this was not possible due to an error with the 'make linux-g ++ - 64'
> command.
>
> I found a solution of this problem here :
> https://sourceforge.net/p/rdock/tickets/7/  (the same error) and
> installed Anaconda and tried to install rDock by command 'conda install -c
> bioconda rdock'  but I obtained another error :
>
> Collecting package metadata (current_repodata.json): done
> Solving environment: failed with initial frozen solve. Retrying with
> flexible solve.
> Solving environment: failed with repodata from current_repodata.json, will
> retry with next repodata source.
> Collecting package metadata (repodata.json): done
> Solving environment: failed with initial frozen solve. Retrying with
> flexible solve.
> Solving environment: -
> Found conflicts! Looking for incompatible packages.
> This can take several minutes.  Press CTRL-C to abort.
> failed
>
>
> UnsatisfiableError: The following specifications were found to be
> incompatible with each other:
>
> Output in format: Requested package -> Available versions
>
>
> What should I do to install rDock correctly? If I install an older
> version of Ubuntu will it work even if this version is no longer supported?
>
>
>
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] How can I install rDock on Ubuntu 18.04?

[Studia S. <stu...@gm...>]

Hello, I am a  begginer Ubuntu user -  I just installed Ubuntu 18.04 on a
virtual machine because I need a rdock for my master's thesis.

I tried to install rDock as per the instructions on the official website
but this was not possible due to an error with the 'make linux-g ++ - 64'
command.

I found a solution of this problem here :
https://sourceforge.net/p/rdock/tickets/7/  (the same error) and installed
Anaconda and tried to install rDock by command 'conda install -c bioconda
rdock'  but I obtained another error :

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with
flexible solve.
Solving environment: failed with repodata from current_repodata.json, will
retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with
flexible solve.
Solving environment: -
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed


UnsatisfiableError: The following specifications were found to be
incompatible with each other:

Output in format: Requested package -> Available versions


What should I do to install rDock correctly? If I install an older version
of Ubuntu will it work even if this version is no longer supported?

[rDock-list-def] build failure on Fedora 30

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

I'm having problems building rDock for source on Fedora 30.
the complete session can be seen here:
https://gist.github.com/tdudgeon/55662d45c19f2d2c68183ab8731c1baa

I can build fine on a Centos7 platform.

Any ideas what's wrong? The error is not too informative.

Thanks
Tim

[rDock-list-def] rDock and Convergence

[Scott B. <sbe...@de...>]

In the main paper, it notes that "System-specific multi-step HTVS protocols
... achieve optimal performance with an average of 8–10 runs per ligand."

I'd be interested in hearing people's experience with optimizing their HTVS
runs.

Also, when rDock writes the pose file, is the order the molecules are
written in commensurate with successive runs? That is, do I expect to see
some sort of convergence or improvement in the score with each later pose
written in the file?

thanks,

Scott



Scott Bembenek, Founder, CEO, CSO
Denovicon Therapeutics <https://www.denovicontx.com/>
San Diego, CA 92130

<https://www.denovicontx.com/>

Re: [rDock-list-def] rDock in HTVS Mode & Grid-based scoring

[Scott B. <sbe...@de...>]

Thanks Markus. I did try this but no luck.

On Mon, Jan 13, 2020 at 7:29 AM Markus Metz <me...@gm...> wrote:

> Scott:
> Is the variable ' RECEPTOR FLEX' in your system defined?
> If yes, can you try and set this value to 0.0 and run your calculation
> again.
> Best,
> Markus
>
> On Sun, Jan 12, 2020 at 9:22 PM Scott Bembenek <sbe...@de...>
> wrote:
>
>> I am looking to speed up rDock when doing an HTVS.
>>
>> I understand that one way to do this (in addition to doing a multistage
>> run, and holding the receptor fixed) is to use the grid-based scoring
>> function.
>>
>> I'm not clear how to implement this actually. Currently, I am using:
>>
>> rbdock -i *input_ligand.sd <http://input_ligand.sd>* -o* lig_docked* -r
>> rdock.prm -p *dock_grid.prm* -n 20
>>
>> However, this results in the error:
>>
>>
>> RBT_INVALID_REQUEST at ../src/lib/RbtVdwGridSF.cxx, line 54
>> Vdw grid scoring function does not support multiple receptor conformations
>> or flexible OH/NH3 groups yet
>>
>> I don't understand this since the receptor is fixed by default and I have
>> not change this option.
>>
>> I did calculate the needed grids rdock_vdw1.grd and rdock_vdw5.grd via
>> rbcalcgrid but am unclear how to actually use them -- which could be part
>> of the problem.
>>
>> Any help would be appreciated!
>>
>> Scott
>>
>>
>>
>>
>>
>> Scott Bembenek, Founder, CEO, CSO
>> Denovicon Therapeutics <https://www.denovicontx.com/>
>> San Diego, CA 92130
>>
>> <https://www.denovicontx.com/>
>>
> _______________________________________________
>> rDock-list-def mailing list
>> rDo...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>>
> --
Scott Bembenek, Founder, CEO, CSO
Denovicon Therapeutics <https://www.denovicontx.com/>
San Diego, CA 92130

<https://www.denovicontx.com/>

Re: [rDock-list-def] rDock in HTVS Mode & Grid-based scoring

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

Scott:
Is the variable ' RECEPTOR FLEX' in your system defined?
If yes, can you try and set this value to 0.0 and run your calculation
again.
Best,
Markus

On Sun, Jan 12, 2020 at 9:22 PM Scott Bembenek <sbe...@de...>
wrote:

> I am looking to speed up rDock when doing an HTVS.
>
> I understand that one way to do this (in addition to doing a multistage
> run, and holding the receptor fixed) is to use the grid-based scoring
> function.
>
> I'm not clear how to implement this actually. Currently, I am using:
>
> rbdock -i *input_ligand.sd <http://input_ligand.sd>* -o* lig_docked* -r
> rdock.prm -p *dock_grid.prm* -n 20
>
> However, this results in the error:
>
>
> RBT_INVALID_REQUEST at ../src/lib/RbtVdwGridSF.cxx, line 54
> Vdw grid scoring function does not support multiple receptor conformations
> or flexible OH/NH3 groups yet
>
> I don't understand this since the receptor is fixed by default and I have
> not change this option.
>
> I did calculate the needed grids rdock_vdw1.grd and rdock_vdw5.grd via
> rbcalcgrid but am unclear how to actually use them -- which could be part
> of the problem.
>
> Any help would be appreciated!
>
> Scott
>
>
>
>
>
> Scott Bembenek, Founder, CEO, CSO
> Denovicon Therapeutics <https://www.denovicontx.com/>
> San Diego, CA 92130
>
> <https://www.denovicontx.com/>
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] rDock in HTVS Mode & Grid-based scoring

[Scott B. <sbe...@de...>]

I am looking to speed up rDock when doing an HTVS.

I understand that one way to do this (in addition to doing a multistage
run, and holding the receptor fixed) is to use the grid-based scoring
function.

I'm not clear how to implement this actually. Currently, I am using:

rbdock -i *input_ligand.sd <http://input_ligand.sd>* -o* lig_docked* -r
rdock.prm -p *dock_grid.prm* -n 20

However, this results in the error:


RBT_INVALID_REQUEST at ../src/lib/RbtVdwGridSF.cxx, line 54
Vdw grid scoring function does not support multiple receptor conformations
or flexible OH/NH3 groups yet

I don't understand this since the receptor is fixed by default and I have
not change this option.

I did calculate the needed grids rdock_vdw1.grd and rdock_vdw5.grd via
rbcalcgrid but am unclear how to actually use them -- which could be part
of the problem.

Any help would be appreciated!

Scott





Scott Bembenek, Founder, CEO, CSO
Denovicon Therapeutics <https://www.denovicontx.com/>
San Diego, CA 92130

<https://www.denovicontx.com/>