acridine orange

From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Thu Mar 19 2009 - 23:54:50 CDT

Dear friends, 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. regards, -- Rudra JRF; SNBNCBS http://www.bose.res.in/~rudra A bus station is where a bus stops. A train station is where a train stops. On my desk I have a work station. Please, if possible, don't send me MS Word or PowerPoint attachments Why?See: http://www.gnu.org/philosophy/no-word-attachments.html Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

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