It's so kind of you to answer my question in such a short time. I'll try other forcefields. Thank you very much! 在 2015-05-11 19:46:27，Justin Lemkul <jalem...@vt.edu> 写道： > > >On 5/10/15 8:48 PM, 范聪 wrote: >> Hello everyone! >> >> I offered a picture called "ask.png" to illistrate my question. >> >> According to the referense papers, the H atom of the -OH group of TYR306 >> should form H_bond with the carbonyl O atom of the ligand. > >Depending on the methods used in those papers, maybe that hypothesis isn't >right :) > >> But in my simulations, the H atom turned after a very short time, towards >> the side chain of PHE152. >> I guess the reason is that, first, the positive Zn ion near the ligand's >> carbonyl O atom made a repulsive effect against the H atom in -OH group; >> second, the π-electron cloud of the side chain of PHE attracted the H atom >> in the -OH group of TYR306. > >I wouldn't put any stock in any arguments about pi electron clouds in MD >simulations. QM/MM shows clearly that the assignment of +2 charge to bound >metals is very crude and often a poor model of reality. > >> As a whole, I failed to make out a real-enough simulation because the >> h_bond between the ligand and TYR306 did not form. >> > >This could also be a force field issue, in general. > >> Also I have one more question: Is there any tools or solutions to >> calculate the hydrophobic or π-π interactions between the ligand and seleted >> residues of the protein, so I could make a graph of the interactions against >> time? >> > >You can map contacts, angles between the rings, etc. See the manual for >available tools and discussions in the archive on these exact topics. > >-Justin > >-- >================================================== > >Justin A. Lemkul, Ph.D. >Ruth L. Kirschstein NRSA Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 629 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 >http://mackerell.umaryland.edu/~jalemkul > >================================================== >-- >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.
