Hi Marlon,
You may have seen the GaMD tutorials here:
https://www.med.unc.edu/pharm/miaolab/resources/gamd/
GaMD-specific questions such as yours should be sent to the GaMD mailing
list. The developers are active and helpful there:
https://sourceforge.net/projects/gamd/lists/gamd-discuss
Good luck!
Best,
Christian
On Thu, Dec 5, 2024 at 2:51 AM Carlos Simmerling via AMBER <
amber.ambermd.org> wrote:
> I suggest contacting the authors directly, they may not read this list.
>
> On Wed, Dec 4, 2024, 1:39 PM Marlon Flor via AMBER <amber.ambermd.org>
> wrote:
>
> >
> > Hello,
> >
> > after trying to run the LiGaMD3 according to the tutorial
> > (
> https://urldefense.com/v3/__https://figshare.com/s/b4cfa9118a5b602faf19__;!!BpyFHLRN4TMTrA!_jifJMPHWBwI9XRXVUDGi4l28bjkE4wPuwaclORSJmGZ_dL3cdW3mKAvqoG6UIWQf7ZwIO11zpZ458kqGA$
> ) I cannot manage yet to
> > obtain the implied functionality of the specific ligand boost, instead I
> > do not get any applied potential at all. I've attached the input
> > configuration file for the equilibration and an abstract from the
> > corresponding output.
> >
> > My protein goes from atom 1 to atom 2803 and the ligand has the resid
> > 186 and the solvated system consists of 43029 atoms.
> >
> > If anybody has used the LiGaMD before and has a hint to get it running,
> > I would appreciate it a lot!
> >
> > Thanks you in advance.
> >
> > Kind regards
> >
> > Marlon_______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
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> >
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Received on Thu Dec 05 2024 - 11:00:02 PST
