On Thu, Jan 12, 2017 at 6:31 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 1/12/17 7:47 PM, Mohsen Ramezanpour wrote: > >> On Thu, Jan 12, 2017 at 4:24 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 1/12/17 3:18 PM, Mohsen Ramezanpour wrote: >>> >>> Dear Gromacs users, >>>> >>>> For parameterization of a molecule in Charmm36, I have got the QM >>>> scanning >>>> and partial charges from GAMMP server. However, the fitted parameters >>>> are >>>> not good enough. >>>> >>>> >>> That's very surprising. What's wrong with what GAAMP gave you? >>> >>> The dihedral has two local minima in both QM and fitted ones both from >> GAAMP. The angle for the minima are okay but the corresponding depths are >> not. >> In fact, the depth for the first local minimum is larger than second one >> in >> QM, while the situation is reverse in MM profile with fitted parameters. >> This makes the dihedral to be more (statistically) in wrong angle (in >> local >> minimum which is not the most favourable one). >> GAAMP, unfortunately, did not work well with my case (some critical >> partial >> charges and critical dihedrals). >> >> >> I decided to do the MM scanning and try to get better parameters for the >>> >>>> dihedral. >>>> >>>> Unfortunately, I do not have any experience with this part, and I could >>>> not >>>> find any tutorial for how to do this in Gromacs. >>>> I was wondering if you are aware of any tutorial which could help me to >>>> overcome this challenging step. >>>> >>>> >>>> Tutorial (CGenFF theory is the same as CHARMM, by design): >>> http://mackerell.umaryland.edu/~kenno/cgenff/download.php#tutor >>> >>> Fitting program and other resources: >>> http://mackerell.umaryland.edu/~kenno/lsfitpar/ >>> http://mackerell.umaryland.edu/ff_dev.shtml >>> >>> Obviously, these are all CHARMM-centric approaches and frankly the >>> modules >>> within CHARMM make parametrization rather straightforward (not "easy," >>> mind >>> you, but straightforward). Since I began working with CHARMM, it has >>> become indispensable in my daily routine. >>> >>> If you want to do things in GROMACS, the main issue is that you will have >>> to do MM scans in a more manual fashion, by restraining the target >>> dihedrals (very strongly) in a series of configurations (typically at >>> intervals of 15 degrees over a full rotation) while allowing the rest of >>> the molecule to relax to match the QM. >>> >> >> If I got it right, I must do EM on the molecule while only the desired >> dihedral is fixed in a specific angle. Which aspect should match with QM? >> If you mean structurally, what is the criteria for matching (RMSD?.)? >> >> > "Match" in this case means "treat equivalently," therefore only one > constraint (restraint in the MM) should be applied while allowing the rest > of the molecule to relax freely. You do have a difficult case because each > of your molecules is symmetric; this means the same dihedral term is > affecting multiple torsions. > So, probably I should 4 dihedrals and try to optimize all at once?!( because all 4 dihedrals of O-C-CH2-CH3 seems equivalent to me). Am I right? > > >> >> Deactivate the restraint, obtain the potential energy of the molecule >> via >> >>> mdrun -rerun and plot as a function of the dihedral. >>> >> >> This should be a zero step EM, right? The molecule should not be allowed >> to >> change its conformation. >> >> > No, a zero-step MD. EM actually changes the coordinates before step zero. > > A bit of shell scripting and careful topology modification and this can >> >>> be done. >>> >>> >> Two more questions on this part: >> 1) I am using the QM scanning data and partial charges from GAAMP. When I >> do this MM scanning, do I need to exclude any 1-4 interactions or I can >> behave this dihedral as other dihedrals? >> > > 1-4 interactions are always at full strength in CHARMM. > > 2) this dihedral is part of a lipid. >> Do I need to do these on only "one Lipid in vacuum" or >> OR >> on all lipids in "a bilayer in vacuum" or in a "bilayer in solvent" >> >> I think it should be "one Lipid in vacuum". >> >> > One model compound in vacuum, from which you will construct the lipid. > How if this compound (which is small part of the lipid) is charged? Should it be still in vacuum? Is there any specific consideration to be made in zero-step MD? e.g. a big simulation box or specific parameter in .mdp file? Thanks Justin for your comments. > > -Justin > > > >>> -Justin >>> >>> There are three parts of molecule which I am interested in its dihedral >>> >>>> parameters that I am stuck in it for a while: >>>> 1) (*2,2-Diethyl-1,3-dioxolane*) >>>> http://www.chemspider.com/Chemical-Structure.217102.html? >>>> rid=378be046-1c14-4bce-ac46-6591776f7e08 >>>> >>>> dihedrals of O-C-CH2-CH3 >>>> >>>> 2) (DIMETHYLPROPYLAMINE) >>>> http://www.chemspider.com/Chemical-Structure.55178.html?rid= >>>> 16e49844-d25d-48c8-b1b5-89fb2f9372bd >>>> >>>> dihedral of CH3-N-CH2-CH2 >>>> >>>> Many thanks in advance for any suggestion. >>>> >>>> Cheers >>>> Mohsen >>>> >>>> >>>> -- >>> ================================================== >>> >>> 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. >>> >>> >> >> >> > -- > ================================================== > > 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. > -- *Rewards work better than punishment ...* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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