Could you please provide little more details about your question. From your question here, I am guessing that your protein doesn't have Mn or Co but you want to add them to the protein. Is that so? That is strange because I think the presence of metal ion won't be just electrostatics, rather they might form a complex with the protein residues. In that case it might be useful to look for a crystal structures of the protein with those ion already present in the system.

Hi,

AMBER has parameters for Mn(II):

http://ambermd.org/

http://sites.pharmacy.manchester.ac.uk/bryce/amber/#ions

So you can do simulations for Mn(II)-containing  proteins.

For Co(II)-containing proteins, MCPB module in AMBER can assist you to do it.

See TUTORIAL A20: Metal Ion Modeling Tutorial

http://ambermd.org/tutorials/advanced/tutorial20/

Thanks Atanu and Yoshinobu. Atanu the crystal structure of the holoprotein is not known. Thats why I wanted to do a MD simulation with both ions and my protein.

Ankita, in the absence of structural data, no one can give you 'coordinates' for the metal ions. That is what you would figure out from your simulations, and therefore figure out their potential coordination partners. What you need for the simulation are the parameters that Yoshinobu has talked about. Although, I am not sure if the typical MD simulation would be good enough for this. Will you be using a QM/MM based method?

Good luck!

Ankita, I agree with Nitesh about the fact that typical MD won't be good enough in this context. I guess your best bet would trying out something like Empirical Valence Bond method but you have to implicitly direct how the coordination with the metal is happening. Here is an article on this method which might be helpful.

http://onlinelibrary.wiley.com/doi/10.1002/0470845015.cu0002/full

I am a novice with these matters and am just testing the QwikMD extension of VMD. In the on line tutorial it is demonstrated how to add topology and parameters, but you need a .str file. I simply modified the one generated by default by my first run with QwikMD and it is attached. I found this information for manganes below in a uiuc thread

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2010-2011/2514.html

So far QwikMD added these MN parameters to its database, but I have not yet attempted a run.

If anyone uses these parameters, please give us all some feedback here. Thanks.

Also if you are an expert you might find some help from this 2013 article

https://www.ncbi.nlm.nih.gov/pubmed/26583865

" Try adding the following to the bottom of your parameter file: MN 0.000000 -0.120000 1.710000 ! ALLOW ION

  Try adding the following to your topology file: at the beginning: MASS 91 MN 54.93804 MN ! manganese 2+

at the end: RESI MN 2.00 ! manganese ion GROUP ATOM MN MN 2.00 PATCHING FIRST NONE LAST NONE "

Just discovered in attempting to generate psf file that I had added the third line above in this str file by copying the MG entry - I had not edited the second and third MG to MN. Here is the corrected file - or just open that one and make the correction yourself.