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Hello Usman-- > I am trying to run a refinement script of an RNA molecule in a > periodic box (explicit water). I firstly tried to produce a script > that will generate water molecules, which I have done. I then made a > script that allowed me to place the RNA molecule inside the water box, > to produce an overlay. > > My problem is that when I run a refinement script on the overlay, the > water molecules do not stay inside the box and disperse away from the > RNA. I think I need a periodic boundary script, that will keep the > water molecules within the box. > I'm not an expert on nucleic acid/water simulations, but I do have a script which will work for proteins. First, the basics: do you have NMR restraints? If not, if would be better to use a different program. We could try a simulation with the current topology/parameters, but they may not be optimal for use with explicit solvent. It may be a good idea to ask the aria people if they have anything along those lines. Another potential issue is the inclusion of counter-ions. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkurdGoACgkQPK2zrJwS/lbmDQCfaTMpiFuA8Edzr4D5tjqA8VM0 G1EAniUlVMURqf/5OL4AaWganRbo5o49 =EbWZ -----END PGP SIGNATURE-----
