[gmx-users] Restraining Protein-ligand distance

[Juan José Galano Frutos]

>
> On 3/27/17 8:42 AM, Juan Jos? Galano Frutos wrote:
> > Hi there,
> >
> > I am trying AFEC simulations in complex (ligand-protein), but sometimes I
> > get the ligands out the binding site, but I dont want that scenary. I was
> > thinking the situation of applying distance retraints between a ligand
> and
> > a protein was already solved in GROMACS version later 5.0... without any
> > necessity of making a hybrid system. But, I'm using version 5.1, and it
> > seems that's not possible doing so, because I'm obtaining errors.
> > Is there currently any happy solution to restraint ligand-protein
> distance?
> > or Has one to still go through the unbrella pulling option to do that?
> >
>
> You need distance as well as orientational restraints.  This is done with
> [intermolecular_interactions], which was a new feature in 5.1.  For
> theory, see
> dx.doi.org/10.1021/ci300505n


>
> -Justin
>

Thank you Justin, very useful help!!!

Juan José

>
> > In the case I need to do a hybrid system what would be a good procedure?
> >
> > Thank you very much.
> >
> >
> > Juan Jos? Galano Frutos
> >
> > Department of Biochemistry and
> > Molecular and Cellular Biology,
> > Faculty of Sciences,
> > University of Zaragoza
> > Pedro Cerbuna # 12, 50009
> > Zaragoza (Spain)
> > +34 976 76 28 06
> >
> > Institute for Biocomputation and
> > Physics of Complex Systems (BIFI)
> > Mariano Esquillor, Edificio I + D - 50018
> > Zaragoza (Spain)
> >
>
> --
> ==================================================
>
> 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 27 Mar 2017 12:57:36 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Regarding Glycine structure
> Message-ID: <1342227d-be3f-89b0-4f44-134a389e6acd at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 3/27/17 8:50 AM, Dilip H N wrote:
> > Thanks Justin,
> >
> > But my doubts are..
> > 1] after energy minimization of both glycine non zwitterionic form and
> > zwitterionic form with water, if i visualize it in vmd, the bond between
> > some of the water molecules are broken.. why is this so..??
>
> http://www.gromacs.org/Documentation/Terminology/
> Periodic_Boundary_Conditions
>
> What you see on the VMD display is its best guess as to how things are
> connected.  That's not always right.  The topology is always right.
> That's why
> trjconv exists.
>
> > 2] and ran nvt,npt,md simulations respectively...and during analysis
> part i
> > am getting only similar two types of RDF graphs...why is this
> happening...i
> > have made all the indexing, etc., proper...
> >
>
> You have provided no useful information about what these RDF plots are or
> how
> you acquired them, so there's no point for either of us in guessing.
> Maybe the
> distribution(s) that you're looking at simply don't vary as a function of
> protonation state.
>
> > Is there any tutorials for these as an example..?? solving this would
> help
> > me a lot....
> >
>
> It's an amino acid in water; it's as easy of a protein system as there is.
> There's nothing special about it that requires a tutorial.
>
> -Justin
>
> >
> >   <https://mailtrack.io/> Sent with Mailtrack
> > <https://mailtrack.io/install?source=signature&lang=en&
> referral=cy16f01.dilip at nitk.edu.in&idSignature=22>
> >
> > On Sun, Mar 26, 2017 at 7:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 3/23/17 2:05 PM, Dilip H N wrote:
> >>
> >>> Hello,
> >>>
> >>> I have a non zwitter ionic glycine molecule [NH2CH2COOH] in water, and
> in
> >>> the first step if i do the energy minimization and then visualizes the
> >>> mixture, the glycine is no more in its pure form as before instead it
> has
> >>> been converted to its zwitter ionic form [NH3CH2COO], and some Hydrogen
> >>> bonds with water are also broken. How can i solve these both issues..??
> >>>
> >>>
> >> Glycine didn't convert between forms.  That's impossible; bonds can't
> >> break or form in a molecular mechanical process.  The termini are
> exactly
> >> what you assigned them to be.  If you want them to be something else,
> you
> >> have to assign them as such with pdb2gmx.  Though you should note that
> NH2
> >> and COOH can't coincide at any real pH value.
> >>
> >> -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
> >>
> >> jalemkul at 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-request at 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 27 Mar 2017 12:58:08 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Extracting Energy of Individual Molecules
>         From Energy File
> Message-ID: <ea72cc3e-fcd9-949a-e16d-ddd61cb2dbc9 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 3/27/17 9:20 AM, Kelechi Okoroafor wrote:
> > Hello, All.
> >
> > Please is it possible to extract the different components of energy (i.e.
> > Bond, Angle, Coulombic and LJ) for individual molecule from the *.edr
> file?
> >
>
> Not from the .edr file, but if you extract the coordinates of that
> molecule from
> the trajectory, create a matching .tpr, and use mdrun -rerun to compute the
> energies.
>
> -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
>
> jalemkul at 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-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 155, Issue 128
> *******************************************************
>