[gmx-users] Protein_ligand simulation

[Justin Lemkul]

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.
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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.
>>
>> Any suggestions?
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>> --
>> *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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