From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Thu Mar 19 2009 - 23:54:50 CDT
i am trying to run a NAMD simulation with the attached molecule. this is a non-std. molecule and hence i have calculated k_b, k_theta for that. but the parameter file needs more spring constants. I am not really interested in long-range interactions.
given this situation, how can i create my parameter file? do i really have to supply k_ub, k_dihedral etc ?
i am working on par_all27_prot parameters. Is some other parameter file will do?
your help is really appreciated.
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