[AMBER] Accelerated md for protein dna complex with modified residue

From: Muthukumaran R <kumaran.bicpu.edu.in>
Date: Tue, 14 Jul 2015 23:35:59 +0530

Dear amber users,

I am working on a protein dna complex with an acetylated lysine. I have
generated the parameters for acetyl-lysine using resp.. I have performed
all-atom simulations, but visualize comformational change which is reported
to occur at large time scale..

My complex is very large (1064 residues) and to sample larger timescale by
conventional md is not possible. So i would like to use accelerated md.
My queries are:
1. Is it possible to perform acemd with modified residues?
2. Is ff99sb force field compatible for acemd of a protein dna complex?
3. Is it necessary to generate multiple trajectories from acemd to see the
conformational changes?
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Received on Tue Jul 14 2015 - 11:30:02 PDT
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