Hi,
I am currently working on MD simulations using NAMD software. I want to visualise the spatial distribution function for my molecules. How to visualise SDF of a molecule? Please suggest me, which software is available for this? I tried in VMD, but not succeeded.
sdf files can be visualized in chimera or pymol. but stile if you are unable to visualize these files then you can convert sdf files to other formats using MARVIN suite which is free...
using this suite you can change format to pdb or mol2 format and then visualize the molecules in chimera...
Dear Tanuj Sharma,
For SDF, what is the file format? I mean it requires PSF cum NAMD trajectory file (dcd file) or pdb cum dcd file?
VMD requires .psf file and trajectory .dcd file...
Open VMD, and load the files .psf and trajectory.dcd. Before clicking Load in the Molecular File Browser window, look at the Frames section. Here you have precise control over how the file is loaded. Leave them at the default setting, so that all frames of the trajectory are loaded.
Dear Tanuj Sharma,
How can I visualize the SDF in the chimera or pymol?. What is the file format?. I mean it requires PSF cum NAMD trajectory file (dcd file) or pdb cum dcd file? kindly suggest
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