[gmx-users] Protein_ligand simulation
RAHUL SURESH
drrahulsuresh at gmail.com
Tue Jul 31 21:09:08 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, 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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>>>>>>>
>>>>>>>
>>>>>> --
>>>>>> *Regards,*
>>>>>> *Rahul *
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
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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
>
> * Please search the archive at http://www.gromacs.org/Support
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--
*Regards,*
*Rahul *
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