Hello to all,
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.
Thank you very much in advance for your help.
G. Rocha
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Received on Tue Jan 09 2024 - 08:30:02 PST
