> I have a problem with autoimage. I have made a Funnel Metadynamics of a
> system in which I have a protein with a metallic atom of ZN2+ and two
> ligands with which I obtain a trajectory in .dcd format. To visualise it
> in VMD, aligning the protein, removing the water and the ions and doing
> the autoimage I have used the following script:
>
> parm topol.prmtop
> trajin trj.dcd
> strip :WAT,Na+,Cl- outprefix noWATnoIONS
> autoimage
> align :1-260.C,CA,N,O first
> trajout md_imaged.crd
>
> The problem is that the autoimage is failing in some way and one of the
> ligands is overlapping with the protein in many frames of the
> trajectory. I don't know if anyone has had the same problem or knows how
> we can solve it.
A question is whether autoimage is failing or if the metadynamics are
allowing bad overlap. I would suggest visualizing directly (without
autoimage) or create some kind of distance measure of ligands to key
residues and see if these look odd or not.
--tec3
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Received on Tue Jan 09 2024 - 18:30:02 PST
