[gmx-users] Protein_ligand simulation
RAHUL SURESH
drrahulsuresh at gmail.com
Tue Jul 31 21:42:19 CEST 2018
Thank you Dr. Justin. With the value of kb, if the unit is KJ/mol nm^2 then
the value is obtained as 624982.
1mDyne/A is 60230KJ/mol nm^2
kb value for f2 molecule from gaussian is 10.3766
On Wed, 1 Aug 2018 at 12:53 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/31/18 3:21 PM, RAHUL SURESH wrote:
> > Adding, while inserting molecule into the system [ gmx insert-molecule ],
> > bond for very few molecules are missing. For instance, in this system I
> > have added 50 molecule and 2 molecule lack bond. After minimization too I
> > can visualize two non bonded fluorine atoms separated by a huge distance.
> > Is this something like visualization error or some mistake that i do in
> my
> > simulation?
> >
>
> Bonds can't break in a classical process. If molecules look distorted,
> they are likely experiencing large forces and therefore are not placed
> judiciously. They are topologically identical by definition, so they
> can't be "missing" bonds.
>
> -Justin
>
> >
> > On Wed, Aug 1, 2018 at 12:39 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
> > wrote:
> >
> >> Thank you Dr. Justin. With the value of kb, if the unit is KJ/mol nm^2
> >> then the value is obtained as 624982.
> >>
> >> 1mDyne/A is 60230KJ/mol nm^2
> >>
> >> kb value for f2 molecule from gaussian is 10.3766
> >>
> >> On Wed, Aug 1, 2018 at 12:20 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >>>
> >>> On 7/31/18 2:48 PM, RAHUL SURESH wrote:
> >>>
> >>>> 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)
> >>>>
> >>> Here's your problem. GROMACS uses SI units. Presumably you've listed
> the
> >>> b0 value in Angstrom, when it should be in nm. Note how your value is
> 10x
> >>> larger than anything else in the file. Check the units on kb, as well.
> >>>
> >>> -Justin
> >>>
> >>>
> >>> 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]
> <https://maps.google.com/?q=%3E%3E+*ERROR+1+%5Bfile+fluorine.itp,+line+21%5D&entry=gmail&source=g>:
> 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
> >>>>>>>>>
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> >>>>>>>>> /Mailing_Lists/GMX-Users_List before posting!
> >>>>>>>>>
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> >>>>>>>>>
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> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>> --
> >>>>>>>> *Regards,*
> >>>>>>>> *Rahul *
> >>>>>>>> --
> >>>>>>>> Gromacs Users mailing list
> >>>>>>>>
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> >>>>>>>> --
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> >>>>>>>
> >>>>>>>
> >>>>>> --
> >>>>> ==================================================
> >>>>>
> >>>>> 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
> >>>>>
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> >>>>> posting!
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> >>>>>
> >>>>>
> >>> --
> >>> ==================================================
> >>>
> >>> 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
> >>>
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> >>>
> >>
> >>
> >> --
> >> *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
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--
*Regards,*
*Rahul *
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