[gmx-users] Protein_ligand simulation

[Mark Abraham]

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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