[gmx-users] Protein_ligand simulation

Justin Lemkul jalemkul at vt.edu
Tue Jul 31 20:08:03 CEST 2018 


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?

> [ 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

> [ 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
>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>
>>>
>>> --
>>> *Regards,*
>>> *Rahul *
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>

-- 
==================================================

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

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

More information about the gromacs.org_gmx-users mailing list