Justin, thanks again for suggestions.
I'm not quite sure how I can use tpbconv -zeroq. For example I want to reduce charges of all amino acids except Asp Glu and His ( to monitor s.b dynamics between that groups only). As I understood -zeroq working with the groups defined in the index file so I should just select all residues that I need in that file, shouldnt it ? Also doest it possible to select pairs of residues placed in the sequence on the distant sites ? (e.g by selecting only pairs within some range of n1 and n2+k where k>n1+10) James 2013/2/2 Justin Lemkul <jalem...@vt.edu>: > > > On 2/2/13 12:18 AM, James Starlight wrote: >> >> 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. >> > > Defining "wrong" is a context-dependent assessment that can only be made > after the fact. You can also probably reduce the number of putative salt > bridges by using tpbconv -zeroq on various groups; there is a threshold > within the g_saltbr program for deciding (based on magnitude of charge) if a > group is a putative salt bridge participant. > > Beyond that, accept the fact that g_saltbr is extremely unwieldy and > post-process accordingly. > > > -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
