Yes, you can go for MODELLER for molecular modelling and GROMACS for dynamics and energy minimization process

i think you can try MODELLOER for minimizing energy.....

i suggest to use GROMACS ( it's free and powerfull ). this software can perform molecular dynamics simulation and energy minimization process and another functions.

Yes, you can go for MODELLER for molecular modelling and GROMACS for dynamics and energy minimization process

u can go with modeller, what if , swiss model and can check ur results..

Thank you Didik, Tannu, Nimrala, Richard & Neetika for your valuable suggestion, GROMACS looks quite feasible to me, i have tried with MODELLER but not getting exact results, leme try GROMACS and i'll share results with you people

Yes, Sybyl and Discovery Studio are probably the best ones, but very expensive. As I know, the only DS software of Accelrys is DS Visualizer, but it does not do protein structure optimization - it is only the browser.

oh, you misunderstood my comment. Of course the Discovery Studio provides it. But it is payable and it often requires access to Pipeline Pilot server, which is also payable. The licence is not so cheap. I just mentioned the free Accelrys software, and only DS Visualizer is free.

Mr. VEERA Chandra i like your idea of using DELHI bioinformatics server, can you help me, how to have access on that server

Yes, I to need to do some work in dynamics. How can I make use of IIT Delhi supercomputing facility?Help me out with proper guidance pls. Tanq.

What about this here? http://swissmodel.expasy.org/

This could be also useful for you.

MOE from Chemical Computing Group is a good package on all these jobs.

MOE is good but slow one .I find working with schrodinger is accurate and robust.

I agree with Didik and suggest GROMACS to use, since it is free and can be installed in your laptop or Desktop. I found GROMACS as a powerful tool.

You can use MODELLER for molecular modeling, which is ranked as number one software in the world. After modelling, it does energy minimization without manual intervention and provide you the lowest energy models with score. GROMACS can be used to minimize the model obtained from MODELLER.

Dear Kanagarajadurai Karuppiah thanks for being so informative, I did used MODELLER but want to have more refined result, now I should be using GROMACS

It''s great job. Hopefully you can success

Sure Muhammad, best wishes for your successful model. Have a great day.

If you've not used GROMACS yet, or just for info... Another quick and free tool is NAMD which does minimization etc. and can use a number of forcefields you use in other modelling programs. Very compatible with VMD if you're that way inclined. See http://www.ks.uiuc.edu/Research/namd/

Also, in case anyone was wanting something a bit quicker and more simple, Chimera (another freebie) also does energy minimization; it uses an AMBER-based energy minimizer. See http://plato.cgl.ucsf.edu/chimera/

whatever the tool/software is used for modelling, the validation of the protein structure is also equally important. There are free validating tools too like procheck, Verify 3D.

That is true. Another good (and free) validation tool out there is Molprobity that I'd recommend which is capable of dealing with both X-ray structures and NMR ensembles. http://molprobity.biochem.duke.edu/

Gromacs

Genno3-d

If you have a fixed backbone template and the intent is to solve for the optimal side chain arrangement then the state of the art is SCWRL. Also you can develop a threading program of your own which selects a random conformer from the rotamer library and superposes it on to your appropriate main chain N-CA-C unit given the residue type. Then perform an energy minimization using CHARMM (see reff: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123238/ )

If you are looking for entirely an ab-initio one, use rosetta (Baker's lab)

Thank you all, Initially I have used CHIMERA for energy minimization and its useful in given case (of 67% Identity), Moreover i have verified results from MolProb as well as from NIH MBI http://nihserver.mbi.ucla.edu/ server and the results are satisfactory!