Helo u can try NAMD with Vegazz software or NAMD with VMD software protein minimisation and molecular dynamics.

Yes, I also second vasavi in using NAMD with vegaZZ, because it is easy to run in windows itself, unlike other molecular dynamics, which requires linux platform

Could you help me acquire these software...i mean are they freely accessible or or they to be purchased with a commercial license..

Hello Sai, look here: molecular modeling on the platform of Pipeline Pilot 8.0 by Accelrys Corp., free software for data visualization and molecular modeling "Discovery Studio Visualizer": http://accelrys.com/products/

Thanks for the information....hope we can catch up later for a better discussion

hi sai,

Try argus lab. Its quite easy to handle. Also is availble free for download (http://www.arguslab.com). otherwise a commercial pack from accelrys called Discovery Studio can be used for better result. It has got many new options also..... or you can use auto dock also..... most of the recent studies shows its maximum usage... it is also a freeware (http://autodock.scripps.edu).

Also gromacs, YASARA, molecular docking server, chiron, AMBER and TINKER are also in the list.....

Also online serverslike firedock, BAPPL.... are available for energy minization, molecular modeling etc....

Thanks a lot yasar...i'm sure your advise will be of immense help...

Yes, NAMD with vegaZZ can be downloaded for free

The above mentioned all software are really good to use for protein energy minimization and visualization purposes.

Thnx to all, but i am actually finding it difficult to download them here, given my inability owing to the prohibition of downloading any software here...

Yet, i'm indebted to all of you and wil soon heed to your advise in right time...

Sai and Vasavi thanks for the valuable participation. It would be valuable if you provide links for NAMD download..

How about using Chimera 1.5.2 with Amber for minimization, does it add something!

you can use either CHARMM, AMBER or NAMD and there are many more which you can use for geometry optimization

of protein....

you can use either Gromacs which can use for geometry optimization of protein