[gmx-users] Protein_ligand simulation

[RAHUL SURESH]

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