[gmx-users] miscelle formation using ligands only

[Phwey Gil]

What does the first line of drg1.itp look like?

On Monday, September 14, 2015, Chetan Puri <chetanpuris at gmail.com> wrote:

> i tried to prepare a topolgy file for my ligands and it contained following
> things,
> #include "gromos43a1.ff/forcefield.itp"
> #include "drg1.itp"
> #include"drg2.itp"
> #include"drg3.itp"
> #include "gromos43a1.ff/spc.itp"
>
> [system]
> miscelle
> [molecules]
> drg1        8
> drg2         5
> drg3         7
> sol           363408
>
>
> But since i have packed the system using PACKMOL intially there were some
> error that no. of coordintaes of gro and top file are not matching since
> intially i took no. of molecules as one for each type but later upon
> changing to the no. as in my packmol input that error had gone and new
> error is showing up
> i.e. Too few parameters in line 1 for drg2.itp
>        Too few parameters in line 1 for drg3.itp
>
> and if i override it with maxwarn than i saw that all the ligands were
> stuck together at one place and also with some different representation .
>
> so can you please help me out with this thing and also is there any other
> way by using gromacs and packing a system of different ligands (gromacs
> version 5.0.4)
>
>
>
> On Sun, Sep 13, 2015 at 6:43 PM, Justin Lemkul <jalemkul at vt.edu
> <javascript:;>> wrote:
>
> >
> >
> > On 9/13/15 3:47 AM, Chetan Puri wrote:
> >
> >> So it means that my topology file should not contain any heading such as
> >> bonds, atoms, dihedral, and should only contain #include drug.itp of
> >> various molecules with system name and number of various molecules.
> >>
> >
> > That's likely the best route, though you can approach it a number of
> > ways.  For a system that is simply a mixture of small molecules, I think
> > this is the cleanest approach, though.
> >
> > Can I just make a box of water.pdb using packmol and use pdb2gmx to
> >> generategenerate a topology with oplsa.ff and include drug.itp files in
> >> that topology file.
> >>
> >>
> > You can, but it's really trivial to do yourself without pdb2gmx:
> >
> > #include "oplsaa.ff/forcefield.itp"
> > #include "oplsaa.ff/tip3p.itp"
> >
> > [ system ]
> > water
> >
> > [ molecules ]
> > SOL     X
> >
> > where X is the number of molecules you have. That's all there is to it.
> >
> > -Justin
> >
> >
> > On Sunday, September 13, 2015, Justin Lemkul <jalemkul at vt.edu
> <javascript:;>> wrote:
> >>
> >>>
> >>>
> >>> On 9/11/15 11:59 PM, Chetan Puri wrote:
> >>>
> >>>>
> >>>> I am using gromacs for the first time . I have installed gromacs 5.0.4
> >>>> version and i want to check a miscelle is formed or not using 5
> >>>> different
> >>>>    ligands in different ratios. I have gone through all basic
> tutorials
> >>>> on
> >>>> how to use gromacs ( lysosyme,protein-ligand).
> >>>>
> >>>> But i am stuck with the problem of having ligands only for simulation
> >>>> due
> >>>> to no force field and topology file.
> >>>>                         I have tried to use packmol to pack a cubic
> box
> >>>>
> >>> with
> >>
> >>> all my different ligands in different ratios and generated a pdb file
> but
> >>>> without making a topology file i am stuck.
> >>>>             So if some one can suggest some possible ways  of doing it
> >>>>
> >>> and i
> >>
> >>> don't have much computational background of manipulating various file
> >>>> extensions of gromacs.
> >>>>
> >>>>
> >>> The only difference here is that you probably aren't going to be using
> >>>
> >> pdb2gmx, so your topology will be one of your own creation.  In
> practice,
> >> the .top is probably just going to amount to a series of #include
> >> statements for the topologies of the various molecules you want to
> study.
> >>
> >>>
> >>> -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 <javascript:;> | (410) 706-7441
> >>> http://mackerell.umaryland.edu/~jalemkul
> >>>
> >>> ==================================================
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> >>
> >>>
> >>>
> > --
> > ==================================================
> >
> > 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 <javascript:;> | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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-- 
Dan Gil
Case Western Reserve University | Class of 2016
Researcher, Department of Chemical Engineering
psg30 at case.edu