Are there any web based or any application for generating input file for MD simulation to be run in NAMD software other than charmm-gui?

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René Hafner

Hi Suraj,

yes, there is.

You can check QwikMD (part of VMD) http://www.ks.uiuc.edu/Research/qwikmd/.

You plug in your pdb (or psf+pdb) file and it can assist you to generate the input files for NAMD.

However, may check the log of charmm-gui or namd to find out what is happening. The NAMD mailing list archive is a good place to find to support.

Kind regards

Harvinder Singh

Suraj Pukhrambam You can try Article Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulati...

it's based on GROMACS.

Easy to use for Beginners