[Openmd-users] openMD

sanan abd sinan1974 at yahoo.com
Wed Dec 7 05:03:46 EST 2016


Dear Daniel the BSA has thiolate ligands. I would like improve my workI m looking for any guide or training. im interestingregard Sinan Adnan AbdulateefPh.D student email: sinan1974 at yahoo.comhand phone: +601111869605school of physics USM 

    On Thursday, November 24, 2016 10:19 PM, Dan Gezelter <gezelter at nd.edu> wrote:
 

 Dear Sinan,

  The first step will be creating a force field. This will define the interactions you want to model in your system.  Gold particles with small molecule ligands have relatively simple force fields, but protein force fields are typically quite complex. If you look in the forceFields directory in the OpenMD distribution, you will see a number of examples. 

The MnM.frc file defines a force field that we used for gold nanoparticles coated with simple thiolate ligands.
The Amber.99.frc file defines the Amber99SB force field which might be appropriate for proteins.  

However, defining cross interactions between the protein atoms and the gold will require a modified force field file that defines all the interactions you want to use.

Best regards,

 —Dan Gezelter


> On Nov 23, 2016, at 11:16 PM, sanan abd <sinan1974 at yahoo.com> wrote:
> 
> Have nice day
> my name Sinan Adnan . i would like to give information about OPenMD. im working to the gold nanoparticles conjugated with bovine serum albumin. 
> can u help me to do software to improve and support  my research work  by using openMD if possible.
> regard  
>  
> Sinan Adnan Abdulateef
> Ph.D student 
> email: sinan1974 at yahoo.com
> hand phone: +601111869605
> school of physics 
> USM



*************************************************************
 J. Daniel Gezelter
 Professor and Director of Undergraduate Studies
 Department of Chemistry and Biochemistry
 251 Nieuwland Science Hall
 University of Notre Dame
 Notre Dame, IN 46556-5670

 gezelter at nd.edu | (574) 631-7595 | http://gezelterlab.org
*************************************************************


   
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