Justin, I suppose that the ussage of the sub-set of trajectories is suitable when you've already known possible salt-bridge pairs. But that time I'd like to obtain that information from my trajectory. E.g I have membrane-embedded protein which is the buddle of alpha-helixes. I want to examine dynamics of the salt-bridges between helixes first of all ( that interactions might serve as the conformation locks ). For such taks I've tried to use smaller -t distance with g_saltbr (e.g considering dynamics of the residues within 1nm assuming both broken and closed salt-bridges as well as taking into account that my protein is membrane-bound where helixes are situated closely than in water-soluble proteins) but again that produced many wrong pairs.
James 2013/2/2 Justin Lemkul <jalem...@vt.edu>: > > > On 2/1/13 3:22 PM, James Starlight wrote: >> >> Dear Gromacs users! >> >> >> I have trajectory from which I want to investigate dynamics of all >> possible salt bridges (E.g distance between adjacent + and - charged >> residues) of my protein during the simulation >> >> As I understood ussage of g_saltbr -t -sep could be suitable for such >> thing but I'm not sure in validness of -t for definition of the native >> salt bridges ( e.g with the default settings g_saltbr produced huge >> number of all possible combinations of the polar contacts within my >> protein ). Is there any others gromacs tols for such investigation? >> > > Not really. If you're looking for any possible combinations of charged > residues, g_saltbr is the only way to go. The default value of -t basically > means everything is always considered, which you may not want. A more > physically relevant truncation distance is probably warranted, but it's been > a long time since I've played with it. You can always make subset > trajectories (with matching .tpr files from tpbconv) to analyze smaller > chunks of residues and ignore things you may not care about, like ions. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
