[gmx-users] Protein_ligand simulation
RAHUL SURESH
drrahulsuresh at gmail.com
Tue Jul 31 20:49:09 CEST 2018
On Tue, 31 Jul 2018 at 11:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/31/18 2:05 PM, RAHUL SURESH wrote:
> > Hi Dr. Mark
> >
> > The itp file is as follows.
> >
> > [ moleculetype ]
> > ; Name nrexcl
> > FLU1 3
> >
> > [ atoms ]
> > ; nr type resnr residue atom cgnr charge mass
> > typeB chargeB massB
> > 1 opls_786 1 FLU1 F 0 0
> > 18.99840
> > 2 opls_786 1 FLU1 F 0 0
> > 18.99840
> >
> > [ bonds ]
> > ; ai aj funct
> > 1 2 1 ; F F
>
> What parameters have you assigned for this bond?
If you are asking in ffbonded.itp, then
F F 1.43363 351456( which I got from previously existing data)
What is the unit for harmonic force constraint (kB) in ffbonded.itp?
The kb value got from vibrational freq analysis is 10.3766 mDyne per
Angstrom
I haven’t added any other parameters to any of the file in Gromacs
>
>
> > [ pairs ]
> > ; ai aj funct
> > 1 2
>
> Why are you assigning a pair interaction? These are for 1-4
> interactions. If you're adding a pair, you're going to get a huge LJ
> repulsion between your atoms that overwhelms the bonded potential, which
> may be the cause of your problem.
>
> -Justin
Yea got it Justin. I will correct it.!
>
>
> > [ angles ]
> > ; ai aj ak funct
> >
> > [ dihedrals ]
> > ; ai aj ak al funct
> >
> > The atom type is chosen based on the sigma and epsilon values from the
> > paper attached to previous mail. [ pre-existing atom type ]
> >
> > The atom didnt move much further but on equilibration the atoms are
> totally
> > dispersed.
> >
> >
> >
> > On Tue, Jul 31, 2018 at 10:58 PM, Mark Abraham <mark.j.abraham at gmail.com
> >
> > wrote:
> >
> >> Hi,
> >>
> >> We can't tell without seeing your molecule type for F2. Presumably
> there is
> >> no bond or the bond is too weak. How far do they move apart?
> >>
> >> Mark
> >>
> >> On Tue, Jul 31, 2018, 14:49 RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
> >>
> >>> Hi.
> >>>
> >>> I obtained the LJ parameters from the paper
> *10.1007/s10765-009-0624-0. [
> >>> OPLS_786 ]*
> >>>
> >>> Add the bond length and harmonic constraints from in ffbonded.itp
> >>>
> >>> The charge is changed to 0 in the itp file and added to .top file.
> >>>
> >>> Minimizations are executed without any error. But on examining the gro
> >> file
> >>> from minimization, the fluorine molecules are broken into atoms. [ ie
> >> they
> >>> atoms move away ]
> >>>
> >>> Why is this happening?
> >>>
> >>>
> >>> On Mon, Jul 30, 2018 at 6:17 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> >>>
> >>>>
> >>>> On 7/30/18 5:54 AM, RAHUL SURESH wrote:
> >>>>
> >>>>> Hello users.
> >>>>>
> >>>>> I overcame the warning errors. The naming is correct now. I tried to
> >>>>> update
> >>>>> the parameters for ffbonded.itp but how will I find the Kb value for
> >>> F-F ?
> >>>> Vibrational frequency analysis.
> >>>>
> >>>> Be careful generating the topology in the manner you have; the F
> >>>> parameters come from trifluoroethanol, so the LJ parameters may not be
> >>> what
> >>>> you want. And the charge of both F atoms in F2 should be set to zero
> >>> (note
> >>>> that TopolGen is a dumb script that just looks for similarity; the
> >>>> resulting topologies often require lots of changes).
> >>>>
> >>>> -Justin
> >>>>
> >>>> On Sat, 28 Jul 2018 at 6:52 PM, RAHUL SURESH <drrahulsuresh at gmail.com
> >
> >>>>> wrote:
> >>>>>
> >>>>> Hi all
> >>>>>> I am performing a simulation between a protein and Fluorine
> >> molecule. I
> >>>>>> have optimized the F2 structure using Gaussian and inserted into the
> >>> box
> >>>>>> using gmx insert-molecules command after adding solvent [gmx
> >> solvate].
> >>>>>> The
> >>>>>> topology for fluorine molecule is generated by topolgen.
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> *[ moleculetype ]; Name nrexclFLU1 3[
> atoms
> >>> ];
> >>>>>> nr type resnr residue atom cgnr charge mass
> >> typeB
> >>>>>> chargeB massB 1 opls_164 1 FLU1 F 0
> >>>>>> -0.206 18.99840 2 opls_164
> >> 1
> >>>>>> FLU1 F 0 -0.206 18.99840
> >> [
> >>>>>> bonds ]; ai aj funct 1 2 1 ; F F[ pairs ];
> >>> ai
> >>>>>> aj funct[ angles ]; ai aj ak funct[ dihedrals ]; ai aj
> >> ak
> >>>>>> al funct*
> >>>>>>
> >>>>>>
> >>>>>> On command gmx grompp -f em.mdp -c alz_F.gro -p alz.top -o ions.tpr
> >> i
> >>>>>> get
> >>>>>> the following errors
> >>>>>>
> >>>>>>
> >>>>>> *ERROR 1 [file fluorine.itp, line 21]: No default Bond types*
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> *NOTE 1 [file alz.top, line 5915]: System has non-zero total
> charge:
> >>>>>> -23.600000 Total charge should normally be an integer. See
> >>>>>> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> >>>>>> <http://www.gromacs.org/Documentation/Floating_Point_Arithmetic>
> >> for
> >>>>>> discussion on how close it should be to an integer.*
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> *WARNING 1 [file alz.top, line 5915]: 16639 non-matching atom names
> >>>>>> atom
> >>>>>> names from alz.top will be used atom names from alz_F.gro will be
> >>>>>> ignored*
> >>>>>>
> >>>>>>
> >>>>>> Indeed there are only 628 atoms in .top file.
> >>>>>>
> >>>>>> Any suggestions?
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> *Regards,*
> >>>>>> *Rahul *
> >>>>>>
> >>>>>>
> >>>> --
> >>>> ==================================================
> >>>>
> >>>> Justin A. Lemkul, Ph.D.
> >>>> Assistant Professor
> >>>> Virginia Tech Department of Biochemistry
> >>>>
> >>>> 303 Engel Hall
> >>>> 340 West Campus Dr.
> >>>> Blacksburg, VA 24061
> >>>>
> >>>> jalemkul at vt.edu | (540) 231-3129
> >>>> http://www.thelemkullab.com
> >>>>
> >>>> ==================================================
> >>>>
> >>>> --
> >>>> 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.
> >>>>
> >>>
> >>>
> >>> --
> >>> *Regards,*
> >>> *Rahul *
> >>> --
> >>> 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.
> >>>
> >> --
> >> 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.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> 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.
>
--
*Regards,*
*Rahul *
More information about the gromacs.org_gmx-users
mailing list