[gmx-users] Protein_ligand simulation

[RAHUL SURESH]

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 ?

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.
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> *[ 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*
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> On command  gmx grompp -f em.mdp -c alz_F.gro -p alz.top -o ions.tpr i get
> the following errors
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> *ERROR 1 [file fluorine.itp, line 21]:  No default Bond types*
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> *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.*
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> *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*
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> Indeed there are only 628 atoms in .top file.
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> Any suggestions?
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> --
> *Regards,*
> *Rahul *
>
-- 
*Regards,*
*Rahul *