[gmx-users] modeling cation-pi box

[Justin A. Lemkul]

EGY wrote:
> Thanks for taking the time to answer, but I think my wording may have confused my question. I shouldn't have used the word box. Within the protein their are several aromatic residues that interact with the small molecule cation. I would like to preserve these interactions throughout the simulations. Is it possible to "enhance" these interactions, since there is no defined force constants that describes these interactions?

The only way to manually maintain these interactions is to use the pull code, 
which does require that some force constant be set.  The other option, of 
course, is to re-derive more suitable parameters.  If the system does not follow 
realistic behavior, then the model must be adjusted in some way.

-Justin

> Thanks.
> Egy
> 
> 
> On Oct 24, 2011, at 12:19 PM, Justin A. Lemkul wrote:
> 
>>
>> EGY wrote:
>>> I am interesting in modeling a small molecule ligand-protein complex that involves a cationic ligand encapsulated by several aromatic residues that form a box around the cation. However, md simulations result in the cation moving outside the box. I am using the CHARMM27 forcefield. Is there a way to restrain the cation portion of the small molecule to within the aromatic box? Or is there a better forcefield, which will take these interactions into consideration.
>> More than likely you simply need to account for periodicity.
>>
>> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>>
>> -Justin
>>
>>> Thanks.
>>> Egy-- gmx-users mailing list    gmx-users at gromacs.org
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>> -- 
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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> 
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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