preparing dsDNA

From: Urszula Uciechowska (
Date: Fri Feb 06 2015 - 05:58:43 CST

Dear NAMd users,

I am trying to prepare a complex od protein and dsDNA. I am having some
problems with DNA, after running psfgn I have visualised obtained psf and
pdb structure and I realised that my GUA-308 and CYT-309 are somehow
connected with a strange long bond. In AMBER I could separate thme by
typing (DG3) for 3' and (DC5) for 5' or TER.
My question is how could I do it in NAMD?
I am using charmm36.nbfix - par_all36.

suggest me something I am new to NAMD.

best regards
Urszula Uciechowska

University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk

Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego

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