Re: vmd-l: Topology for drugs to do MD after docking

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Oct 21 2015 - 14:44:18 CDT

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Nikhil,

I have found that the best way for generating a PSF file of small molecules from coordinates is to use the TopoTools API. There is extensive documentation on Axel’s website (https://sites.google.com/site/akohlmey/software/topotools).

Regards,
Christopher Mayne


On Oct 21, 2015, at 11:40 AM, Nikhil Maroli <scinikhil_at_gmail.com<mailto:scinikhil_at_gmail.com>> wrote:

Dear users,
i want to do MD of protein and drugs together after docking,i done the docking part now when i try to create psf file there is topology problem so anyone can tell me how to solve this problem-how to get the topology parameter for drugs ?
Thanks in advance

--
Ragards,
Nikhil Maroli

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