[gmx-users] Protein_ligand simulation
RAHUL SURESH
drrahulsuresh at gmail.com
Tue Jul 31 21:21:49 CEST 2018
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?
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
>>>>>>>>
>>>>>>>> * Please search the archive at http://www.gromacs.org/Support
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>>>>>>>>
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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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>>>> 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
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
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>>
>
>
>
> --
> *Regards,*
> *Rahul *
>
--
*Regards,*
*Rahul *
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