Hi, Firdous, Most modern force fields have a way to describe ions, small molecules or modified residues for MD run. And they already contain description for phosphorilated aminoacids. So you can choose whichever you want. But it is more appropriate to ask in the specialized mailing list, like CCPBioSim <http://www.ccpbiosim.ac.uk/>.
пт, 28 февр. 2020 г. в 07:01, Firdous Tarique <kahkashantari...@gmail.com>: > Hello everyone > > I am trying to run a molecular dynamics simulation of a protein which has > a Zn atom and few phosphorylated PTMs (Thr is phosphorylated). PTMs and Zn > play essential roles to maintain the structural integrity and therefore > cannot be removed rather I want to keep both of them for my run. I facing a > problem in choosing a force field where running the program keeping both > the molecules is not a problem. > > Kindly suggest me how to proceed with this molecular dynamics run. > > Best > > Kahkashan > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > -- Evgenii Osipov Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, KU Leuven O&N2 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
