shahid nayeem wrote:
Dear all
I am interested in simulating a model protein with cobalt forming
coordinate bond with His. I coud'nt find entry for cobalt in any
forcefield .rtp file. I am using Gromacs 4.5.4 . If any one can help me
in getting forcefield parameters for charmm27/ OPLSaa/Amber99 in gromacs
format please respond. Please suggest where else I should search for these.
Standard, non-polarizable MM force fields are not particularly well-suited for
dealing with transition metals. Fixed point charges on such species, especially
those coordinated to amino acids, are generally very incorrect, not to mention
geometric coordination parameters that are not built-in.
http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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