[gmx-users] Protein_ligand simulation

Justin Lemkul jalemkul at vt.edu
Tue Jul 31 20:51:10 CEST 2018 


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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>>>>>>
>>>>>
>>>>> --
>>>>> *Regards,*
>>>>> *Rahul *
>>>>> --
>>>>> 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
>>
>> ==================================================
>>
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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

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

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