NAMD 2.9 Changing/Replacing atoms in multiple molecules

From: Michal Skoczek (
Date: Fri Feb 21 2014 - 08:02:41 CST

Hi all,

I have quite strange problem... I would like to replace atoms (f.ex from C
(carbon) to N (nitrogen) in multiple molecules of one type in my files. Is
it possible at all? I just want to change them in already created system
thats why MOLEFACTURE is not the answer. It allows me to change only
system up to 200 atoms - mine has 56000.Anyone has an idea how to do it?

I can provide any details that seem relevant. Any help regarding this
subject would be greatly appreciated!

Many thanks,
Michal Skoczek
PhD Student

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