[gmx-users] Protein_ligand simulation

Justin Lemkul jalemkul at vt.edu
Tue Jul 31 21:23:26 CEST 2018 


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]:  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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>>>>>>>>> or
>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>
>>>>>>>>>
>>>>>>>> --
>>>>>>>> *Regards,*
>>>>>>>> *Rahul *
>>>>>>>> --
>>>>>>>> Gromacs Users mailing list
>>>>>>>>
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>>>>>>>> posting!
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>>>>>>>>
>>>>>>>> --
>>>>>>> Gromacs Users mailing list
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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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>>>>>
>>>>>
>>> --
>>> ==================================================
>>>
>>> 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

==================================================

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