Grid-based VdW Scoring Option

[Arthurcarre]

Hello !

Despite the documentation and my research on the forums, I still don't know how to use the docking protocols dock_grid.prm and dock_solv_grid.prm. On one of the forums, I found this post dated on 2020-01-17, which mentions the difficulties I'm having too.

Please found the content of this post just here:

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 -o ligand_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. And to be sure, I did set RECEPTOR_FLEX to 0.0 in the rdock.prm -- still no luck.

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!

Using the example files in your tests, could you, please, bring me an example to illustrate the different command lines to apply in order to use the docking protocol dock_grid.prm ?

Looking forward to your guidance on this matter,

Best regards,
Arthur

[xbarril]

Been a long time since I used this option, as the gain in efficiency is small. But I’ve tried now and it works for me STEPS: rbcalcgrid -o_vdw1.grd -rmy.prm -pcalcgrid_vdw1.prm rbcalcgrid -o_vdw5.grd -rmy.prm -pcalcgrid_vdw5.prm rbdock -i lig.sd -o lig_docked_grid.sdf -r my.prm -p dock_grid.prm -n 20 Make sure to set: RECEPTOR_FLEX 0.0 in ‘my.prm’ xb On 26 Feb 2024, at 09:06, Arthurcarre ***@***.***> wrote: Hello ! Despite the documentation and my research on the forums, I still don't know how to use the docking protocols dock_grid.prm and dock_solv_grid.prm. On one of the forums, I found this [post] (https://sourceforge.net/p/rdock/tickets/9/) dated on 2020-01-17, which mentions the difficulties I'm having too. Please found the content of this post just here: 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 -o ligand_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. And to be sure, I did set RECEPTOR_FLEX to 0.0 in the rdock.prm -- still no luck. 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! Using the example files in your tests, could you, please, bring me an example to illustrate the different command lines to apply in order to use the docking protocol dock_grid.prm ? Looking forward to your guidance on this matter, Best regards, Arthur — Reply to this email directly, view it on GitHub<#92>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACH7XJXSUMYCLDNORKQ7473YVQ7BDAVCNFSM6AAAAABDZWRQROVHI2DSMVQWIX3LMV43ASLTON2WKOZSGE2TGNJSGE3TMOA>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir informació confidencial o protegida legalment i s’adreça exclusivament a la persona o entitat destinatària. Si no consteu com a destinatari final o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu del sistema tant el missatge com els fitxers adjunts que hi pugui haver. Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no consta como destinatario final ni es la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a revelar su contenido. Si lo ha recibido por error, informe de ello al remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos que pueda contener. This email message and any attachments it carries may contain confidential or legally protected material and are intended solely for the individual or organization to whom they are addressed. If you are not the intended recipient of this message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any part of it. If you have received the message by mistake, please inform the sender of this and eliminate the message and any attachments it carries from your account.

[Arthurcarre]

I tested it and it works. Thank you very much !

Best regards,
Arthur