VMD-L Mailing List

From: Emma Wu (ewu20_at_illinois.edu)
Date: Thu Oct 15 2020 - 00:50:30 CDT

Hi all,
I have a molecule that I have fragmented and parameterized each fragment
using ffTK. I am now trying to combine the fragments but I am unsure how I
should proceed. I have overlapping fragments that include the linker
portion.

Here are the things I am confused about:
1. Since I have the linker portions optimized through overlapping
fragments, how would I combine that information into the pdb, psf, and par?

2. How would I get a new pdb of the full molecule from fragments pdbs that
I have optimize?

Thank you so much for all and any suggestions!

Best,
Emma