Dear All,
I performed one MD simulation on triiodothyronine (T3) and its target
protein. This molecule has three iodine atoms and I use sqm from
ambertools 1.5 to assign AM1-BCC charge for T3. One reviewer thought that
AMB-BCC charge is known to be quite inaccurate. This is one of key
technical questions for the rejection of my publication.
After MD simulations, I performed RAMD simulations and RAMD simulations
revealed some dissociation pathways, some of them were verified by previous
relevant papers. I think the parameters no problem. The reviewer kindly
asked me yo provide some quantitative indications that the parameters
obtained yield reliable or reasonable behavior for the T3 molecule. Could
anybody tell me how to prove that AM1-BCC charge is reasonable for T3?
Kind regard
Shulin
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 08 2013 - 18:00:03 PST
