You should check the Q&A section, this question was risen a lot of times before. For minimization you can use standalone soft (GROMACS, Amber, Chimera etc.), as well as online servers (Yasara, Chiron etc.).

Yes, it's recommended to minimize structures from PDB to remove clashes, bad angles etc. But once again, look through the Q&A for details.

Dear Sajin, the tool below concerns the hospitality sector but you might find it useful:

The Hotel Energy Solutions (HES) e-Toolkit is supported by the Intelligent Energy – Europe (IEE) program which is giving a boost to clean and sustainable solutions (http://ec.europa.eu/energy/intelligent/). HES enables Small and Medium Enterprises (SMEs) in the accommodation sector to assess their current energy use and carbon footprint against similar enterprises and provide support in ranking practical and cost-effective energy efficiency and renewable energy investment options.

Sergii Vakal,

Thanks for the  answer sir

Is there any windows based tool for energy minimizatoion?I used ABALONE. but its showing some errors !!  

Is itt necessary to remove ligands from the stucture ?I am using a reference ligand in the pdb structure for finding active site.  So if ligand is removed from structure, finding out that active site will be tough? 

PDB do not assess the submitted structures. There are a lot of garbage in PDB. So, you must check the structure before you use it for further analysis. They have addressed this issue in this article:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3195755/

You might also use this developmental version of the PDBe interface where they have implemented the validation tools:

http://wwwdev.ebi.ac.uk/pdbe/entry/search/index

The search here provides the information about the model quality.

You must remove the ligand from the structure before docking. Isn't it obvious? By not removing the ligand you are actually blocking the space. Your test ligand cannot bind to the active site if the reference ligand is still there.

https://www.ebi.ac.uk/training/sites/ebi.ac.uk.training/files/materials/2014/140407_EMBO/6_-_pdbe_validation_-_john_berrisford.pdf

Dear Sajin,

If you want Windows-compatible tool, I can recommend you UCSF Chimera (http://www.cgl.ucsf.edu/chimera/). It's very nice software for different molecular modeling tasks, including energy minimization. Of course, you should edit the protocol for your needs, but for my models it usually works well. There is also an energy minimization module in DeepView, but I can't recommend it since it can't be adjusted.

Some web-servers can also be helpful (Yasara Minimiation Server, Chiron etc.), but it's not so important which tool you will use, the most important is HOW (protocol, force field etc.).

Sergii Vakal 

Thanks sir. let me check out  UCSF Chimera. If i got any doubts i will contact you

with regards

Sajin

Uttam pal,

i need reference ligand for predicting its active site. I am using Argus lab for docking.

After predicting the biding site, i will delete that reference ligand and carry out docking.

But till prediction of binding site i need reference ligand. hope u get my point?

with regards

Sajin

You can check PRODRG server which instantly optimizes the structure.

There is also an energy minimization module in SPDBV

Hello Sajin A K

Energy minimization is crucial during your in silico works, because, as Uttam Pal has mentioned, PDB doesn't evaluate the structures it receives, for errors. This paper will help you understand that:

DOI: 10.1038/343687a0

I shall recommend you 3 of the best energy minimization servers available online, accounting the fact that, they are being used by many researchers in their works:

• Moderefiner:

http://zhanglab.ccmb.med.umich.edu/ModRefiner/

• Yasara:

http://www.yasara.org/minimizationserver.htm

• Chiron :

https://dokhlab.med.psu.edu/chiron/processManager.php

Hope it helps.

Article Top-down free-energy minimization on protein potential energ...

You can use Swiss PDB Viewer. It is free software.

Avogadro software, though it is pretty buggy, might help you minimize the free energy of a molecule.