We've recently announced iCing, which includes whatif as well. Please, take a look at http://nmr.cmbi.ru.nl/cing/Home.html. If it happens that your complex is from NMR and deposit in PDB so you can find it here (http://nmr.cmbi.ru.nl/NRG-CING/index/index.html) already evaluated.
Cheers, Alan On Fri, Apr 3, 2009 at 11:00, <[email protected]> wrote: > > Chih-Ying Lin wrote: > > > > > > > > HI > > The program WHATIF can perform a proper validation of the structure. > > But, it is not free software. > > > > Can anyone tell me how to test the protein structure manually or by > Gromacs? > > > > What is the criteria to determine the quality of the structure? > > That depends on your objective - but you have to define that. Ultimately > some protein structure generated by a piece of software has to match in > a relevant way the structure found in biological systems. What that > means varies with what experimental information you have available. > Various computational tools might assist in estimating that match. > > Mark > > -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<<
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
