Thanks Justin Can you please suggest me any article or reading that can help me to understand the factors to be considered while choosing a force field or to parameterize the ligand?
On 1 Mar 2018 18:14, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 3/1/18 8:03 AM, neelam wafa wrote: > >> Dear gmx users >> >> I am trying to run a protein ligand simmulation. How can i create topolgy >> for ligand. prodrg topology is not reliable then which server or software >> can be used? can topology be created by T LEEP off ambertools package for >> gromacs?? >> > > The method you use depends on the parent force field you've chosen. The > PRODRG and ATB servers are for GROMOS force fields, GAFF methods (RED > server, antechamber, etc) are for AMBER. ParamChem/CGenFF are for CHARMM. > You can't mix and match. You need to do your homework here to make sure > that the force field you've chosen for your protein is an appropriate > model, as well as whether or not you can feasibly parametrize your ligand > (not an easy task and generally not advisable for a beginner, because you > should *never* trust a black box and always validate the topology in a > manner consistent with the parent force field). > > secondly how to select the boxtype as I am new to simmulation so cant fix >> the problem. Please also guide me what factors should be considered to >> select the water model?? >> > > The water model is part of the force field; each has been parametrized > with a particular model (though some do show some insensitivity if changed, > but again this is your homework to do before ever thinking about doing > anything in GROMACS or any other MD engine). > > The box shape has no effect as long as you set up a suitable box-solute > distance that satisfies the minimum image convention. You can use non-cubic > boxes to speed up the simulation if it's just a simple protein (complex) in > water. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.