From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Sat Oct 17 2015 - 15:42:11 CDT
Yes, you could retain initial position of halide ions, but during
simulation it is expected that such ions could move to solvent or
similar. In any way it is strongly recommendable to learn from basic
NAMD tutorials available at:
http://www.ks.uiuc.edu/Training/Tutorials/namd-index.html how to set-up
input for and to run basic NAMD simulations.
On 10/17/2015 10:31 PM, Stojanoski, Vlatko wrote:
> Hi Branko,
> Thank you for all the suggestions. I'm looking forward to explore all
> of them.
> I'm sorry but I forgot to add that the halide ions are already in the
> crystal structure and I would like to retain them and follow their
> movement through out the course of the simulation. Will I be able to
> do that with the things that you mentioned? Keep the ions from the
> structure and hydrate the system.
> Also, If I download the parameter files from
> http://mackerell.umaryland.edu/charmm_ff.shtmlI can just add them in
> the Parameter files tab in the NAMDgui? I'm not very familiar with the
> actual steps about how it works.
> Thank you again for your help!
> All the best,
> *From:* Branko <bdrakuli_at_chem.bg.ac.rs>
> *Sent:* Saturday, October 17, 2015 2:35 PM
> *To:* namd-l_at_ks.uiuc.edu; Stojanoski, Vlatko
> *Subject:* Re: namd-l: Performing MD simulations with protein and
> halide ions (iodide, bromide, chloride)
> CHARMM force field support majority of halide ions (for example
> Clminus is commonly used as counter ion to 'neutralize' positively
> charged protein). So, you should look in parameter files available
> from http://mackerell.umaryland.edu/charmm_ff.shtml
> CHARMM force field parameters - MacKerell Lab
> Additive Force Field Files. Toppar files included with C37 and later
> versions of CHARMM include the C36 additive protein, nucleic acid,
> lipid, and carbohydrate ...
> Read more... <http://mackerell.umaryland.edu/charmm_ff.shtml>
> Also see: http://www.ks.uiuc.edu/Research/vmd/plugins/autoionize/
> Alternatively, you could use VegaZZ as GUI
> (http://nova.disfarm.unimi.it/cms/index.php?Software_projects:VEGA_ZZ). In
> this software preparation of NAMD input (including addition of ions)
> is really user-friendly
> On 10/17/2015 9:05 PM, Stojanoski, Vlatko wrote:
>> Dear NAMD users,
>> I'm relatively new to the MD simulations and previously I have
>> managed to perform MD simulations of proteins in a solvent box with
>> the NVT ensemble using the NAMD Graphical interface in VMD.
>> However, now I'm trying to perform simulations of proteins that
>> interact with halide ions (iodide, bromide, and chloride in
>> particular) and I'm not sure how to go about it. I know that I need
>> to create parameters for the ions but not sure how. Any help or
>> pointing in the right direction are greatly appreciated. Thank you
>> All the best,
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