Custom calculation of forcefields for ligands in Isolde
Dear ChimeraX and Isolde experts, I am trying to parameterize a ligand in Isolde 1.6 in order to fit it into my density. The ligand conforms to the requirements that are outlined in the manual (not covalently bound, only consists of certain elements, etc). However, parameterizing the residue using the inbuilt ANTECHAMBER/AMBER utility times out unfortunately, with an error saying that convergence in SCF cannot be reached. Upon investigating the issue I learned that it could be possible to avoid this error with adjusted command line parameters for AMBER in order to let it run longer for correct values. My question is: Is it possible to pass custom flags or command line arguments from Isolde to AMBER in ChimeraX? And if yes, how? The default command ‘Isolde parameterize residue’ does not seem to have any AMBER specific options. For example, how can I add 'adding ndiis_attempts=700’ (or other modifications) to my input sqm file? Thank you in advance, Paul
That's a very good idea, which unfortunately I haven't implemented. The code behind that command (that actually runs ANTECHAMBER) is mostly just the ChimeraX code underlying `addcharge` - I'll have to double-check with Eric, but I think implementing this will require that ChimeraX code to provide arguments passing those parameters through. -- Tristan On Thu, Nov 9, 2023 at 4:40 AM Paul Sauer via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX and Isolde experts,
I am trying to parameterize a ligand in Isolde 1.6 in order to fit it into my density. The ligand conforms to the requirements that are outlined in the manual (not covalently bound, only consists of certain elements, etc). However, parameterizing the residue using the inbuilt ANTECHAMBER/AMBER utility times out unfortunately, with an error saying that convergence in SCF cannot be reached. Upon investigating the issue I learned that it could be possible to avoid this error with adjusted command line parameters for AMBER in order to let it run longer for correct values. My question is: Is it possible to pass custom flags or command line arguments from Isolde to AMBER in ChimeraX? And if yes, how? The default command ‘Isolde parameterize residue’ does not seem to have any AMBER specific options. For example, how can I add 'adding ndiis_attempts=700’ (or other modifications) to my input sqm file?
Thank you in advance,
Paul
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Actually, looking back through my code it turns out that while I *modelled* it on the addcharge code, it's independent of it. Will see about exposing those parameters to the command line. On Thu, Nov 9, 2023 at 4:34 PM Tristan Croll <tcroll@altoslabs.com> wrote:
That's a very good idea, which unfortunately I haven't implemented. The code behind that command (that actually runs ANTECHAMBER) is mostly just the ChimeraX code underlying `addcharge` - I'll have to double-check with Eric, but I think implementing this will require that ChimeraX code to provide arguments passing those parameters through.
-- Tristan
On Thu, Nov 9, 2023 at 4:40 AM Paul Sauer via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX and Isolde experts,
I am trying to parameterize a ligand in Isolde 1.6 in order to fit it into my density. The ligand conforms to the requirements that are outlined in the manual (not covalently bound, only consists of certain elements, etc). However, parameterizing the residue using the inbuilt ANTECHAMBER/AMBER utility times out unfortunately, with an error saying that convergence in SCF cannot be reached. Upon investigating the issue I learned that it could be possible to avoid this error with adjusted command line parameters for AMBER in order to let it run longer for correct values. My question is: Is it possible to pass custom flags or command line arguments from Isolde to AMBER in ChimeraX? And if yes, how? The default command ‘Isolde parameterize residue’ does not seem to have any AMBER specific options. For example, how can I add 'adding ndiis_attempts=700’ (or other modifications) to my input sqm file?
Thank you in advance,
Paul
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-- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
Thank you, Tristan. If you should indeed implement it, I'd surely make a lot of use of it! Best Paul On Thu, Nov 9, 2023, 08:50 Tristan Croll <tcroll@altoslabs.com> wrote:
Actually, looking back through my code it turns out that while I *modelled* it on the addcharge code, it's independent of it. Will see about exposing those parameters to the command line.
On Thu, Nov 9, 2023 at 4:34 PM Tristan Croll <tcroll@altoslabs.com> wrote:
That's a very good idea, which unfortunately I haven't implemented. The code behind that command (that actually runs ANTECHAMBER) is mostly just the ChimeraX code underlying `addcharge` - I'll have to double-check with Eric, but I think implementing this will require that ChimeraX code to provide arguments passing those parameters through.
-- Tristan
On Thu, Nov 9, 2023 at 4:40 AM Paul Sauer via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX and Isolde experts,
I am trying to parameterize a ligand in Isolde 1.6 in order to fit it into my density. The ligand conforms to the requirements that are outlined in the manual (not covalently bound, only consists of certain elements, etc). However, parameterizing the residue using the inbuilt ANTECHAMBER/AMBER utility times out unfortunately, with an error saying that convergence in SCF cannot be reached. Upon investigating the issue I learned that it could be possible to avoid this error with adjusted command line parameters for AMBER in order to let it run longer for correct values. My question is: Is it possible to pass custom flags or command line arguments from Isolde to AMBER in ChimeraX? And if yes, how? The default command ‘Isolde parameterize residue’ does not seem to have any AMBER specific options. For example, how can I add 'adding ndiis_attempts=700’ (or other modifications) to my input sqm file?
Thank you in advance,
Paul
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
participants (3)
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Paul Sauer -
Paul Victor Sauer
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Tristan Croll