Is there any free online server where i can do simulation of .pdb file of protein for more than 10 ns?
Mr. Gupta,
You do not need free on-line server to compute your protein by MDs. Depending on the theoretical MD levels a significant part of the computations (even more then 90-95 %) can be done in your personal computer; using even free of charge program packages; accounting for the fact, in addition, that a large part proteins in ProteinDataBank do not exceed 15000-20000 atoms (There are known about 100000 structures). Even, the systems often are significantly smaller.
It should be mentioned, here that there are available large set MD methods allowing you to balance the computational time/costs and accuracy. So, only for those systems, which represent for your study a significant importance you could use the server of your Institution.
A list of free of charge program packages can be found here:
https://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling
Because of I have met similar question in RG, I have obtained computational data (attachment) using 5 combinations of MD methods. Please bear in mind that the shown data are obtained by methods which are, generally, slower. Moreover there are almost more then 20 additional combinations of methods which to provide you a reliable information at a significantly reduced computational cost.
You can see, the data about two independent systems NH4+...H2O and H2O...H2O (a neutral system and a charged one) by 5 independent methods (some of them with a good-to-excellent accuracy, themselves) have shown same energetics behavior as a function of the method. In other words, you have obtained different energies (ETOT is given only as attachment) but the difference is approximatively same for both independent systems. It is shown by const (c1).
In addition, there are shown MM/MD computations of crystal sructure of beta2AR (4487 heavy atoms; 6478 atoms; 24593 electrons), for example (309g.pdb [1]).
These results indicated that, even using a lower as accuracy method, you have received meaningful as energetics behavior information about the interacting systems. And this information is representative to other systems as well. Therefore the analytical information about the energetics is comparable and representative to other molecular systems. Or you can compare data of set systems, which are results of independent computations.
Nevertheless, even if you presumably have obtained a high accuracy computing an "exact" energy, there is a question about the experimental methods which you shall use comparing your "absolute" theoretical data for proteins with the experiment? In addition to, which experimental technique shall be used, determining the quantity, which should be compared with the theoretical value?
sir please refer Movie Maker: a web server for rapid rendering of protein motions and interactions .Journal ListNucleic Acids Resv.33(Web Server issue); 2005 Jul 1PMC1160245
Mr. Gupta,
You do not need free on-line server to compute your protein by MDs. Depending on the theoretical MD levels a significant part of the computations (even more then 90-95 %) can be done in your personal computer; using even free of charge program packages; accounting for the fact, in addition, that a large part proteins in ProteinDataBank do not exceed 15000-20000 atoms (There are known about 100000 structures). Even, the systems often are significantly smaller.
It should be mentioned, here that there are available large set MD methods allowing you to balance the computational time/costs and accuracy. So, only for those systems, which represent for your study a significant importance you could use the server of your Institution.
A list of free of charge program packages can be found here:
https://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling
Because of I have met similar question in RG, I have obtained computational data (attachment) using 5 combinations of MD methods. Please bear in mind that the shown data are obtained by methods which are, generally, slower. Moreover there are almost more then 20 additional combinations of methods which to provide you a reliable information at a significantly reduced computational cost.
You can see, the data about two independent systems NH4+...H2O and H2O...H2O (a neutral system and a charged one) by 5 independent methods (some of them with a good-to-excellent accuracy, themselves) have shown same energetics behavior as a function of the method. In other words, you have obtained different energies (ETOT is given only as attachment) but the difference is approximatively same for both independent systems. It is shown by const (c1).
In addition, there are shown MM/MD computations of crystal sructure of beta2AR (4487 heavy atoms; 6478 atoms; 24593 electrons), for example (309g.pdb [1]).
These results indicated that, even using a lower as accuracy method, you have received meaningful as energetics behavior information about the interacting systems. And this information is representative to other systems as well. Therefore the analytical information about the energetics is comparable and representative to other molecular systems. Or you can compare data of set systems, which are results of independent computations.
Nevertheless, even if you presumably have obtained a high accuracy computing an "exact" energy, there is a question about the experimental methods which you shall use comparing your "absolute" theoretical data for proteins with the experiment? In addition to, which experimental technique shall be used, determining the quantity, which should be compared with the theoretical value?
Additional computations to a discussion using ab initio ADMP with ONIOM of proteins in the same topic:
https://www.researchgate.net/post/Is_there_any_free_online_server_to_carry_out_molecular_dynamic_simulation_of_protein_along_with_ligands?_tpcectx=profile_answers
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