[gmx-users] Protein_ligand simulation
RAHUL SURESH
drrahulsuresh at gmail.com
Tue Jul 31 20:05:43 CEST 2018
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
[ pairs ]
; ai aj funct
1 2
[ 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
> > >
> > > ==================================================
> > >
> > > --
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> >
> >
> >
> > --
> > *Regards,*
> > *Rahul *
> > --
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--
*Regards,*
*Rahul *
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