If you want to observe H-bond dynamics and do it with an atomistic precision than, of course, you need an all-atom representation. United atoms will still *effectively* account for H-bonding, if you are happy with reduced precision.
Dr. Vitaly Chaban On Wed, May 29, 2013 at 8:01 AM, Revthi Sanker <[email protected]>wrote: > Dear Sir, > I would like to express my deepest gratitude for patiently reading my > query. I am simulating the cholesteryl ester transfer protein ( the crystal > structure has 4 bound lipids). I propose to study the inhibitor induced > changes in the conformation of protein and the bound lipids. I am assuming > unless I perform an all-atom simulation, I will be missing out some > crucial interactions like H-bond formation and breaking. Kindly let me if > my understanding is wrong. > Thank you so much once again for the reply, > Revathi > > --- On *Tue, 28/5/13, Dr. Vitaly Chaban <[email protected]>* wrote: > > > From: Dr. Vitaly Chaban <[email protected]> > Subject: Re: choice of force field -reg > To: "Revthi Sanker" <[email protected]>, [email protected] > Date: Tuesday, 28 May, 2013, 4:14 PM > > without knowing full details of your simulated system and the goals you > pose, I cannot advise anything more definite than I did before. > > if I were you and my system were yours, I would start with MARTINI FF. > > I wish you a success in your endeavor. > > Dr. Vitaly Chaban > > > > > On Tue, May 28, 2013 at 6:11 PM, Revthi Sanker > <[email protected]<http://mc/[email protected]> > > wrote: > > > > Dear Sir, > Thank you so much for your reply. To be specific, my system has only four > lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I was > not able to get all atom paramters for these lipids from the lipid book( > only united atom parameters were available). So I had resorted to using > united atom for the whole system. But I am afraid if I am missing out on > some crucial protein-drug interactions because of this united atom > consideration. > Kindly guide me in this regard. > Thank you so much once again. > > Yours sincerely, > Revathi > M.S.Research Scholar > Indian Institute of Technology Madras > India > > > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
