From: Urszula Uciechowska (urszula.uciechowska_at_biotech.ug.edu.pl)
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
Poland
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http://www.ug.edu.pl/
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