[gmx-users] Request on help in ED method

[Dmitry Egorov]

 From
Dmitry A. Egorov, post-graduate of
Department of Clinical Laboratory
and Microbiological Diagnostics
Ural State Medical Academy
620219 Yekaterinburg, Repin str., 3,
Russia
E-mail : egorov at newhospital.ru

To Gromacs software users mailing list
E-mail : gmx-users at gromacs.org

   Dear Colleagues, happy holidays, and please help me in understanding of
ED method.

   In our laboratory we try to understand functioning of some enzymes on the
base of their structures. Particularly we
want to study possible changes in proteins conformations by using CONCOORD
and Essential Dynamics techniques.

  Unfortunately I am novice in molecular modelling and have a lot of
difficulties with application these methods in
my work and with understanding some conceptions. And I found that
description of Essential Dynamics methods that
made in Gromacs User Guide v3.1.1 is too brief for me. So could you help me
and give me more detailed description
as answer to my questions. Again, unfortunately I did not understand clearly
main algorytms of ED method ( what to do to obtain needed results ) from
article D. M. F. Van AALTEN, B. L. De GROOT, J. B. C. FINDLAY, H. J. C.
BERENDSEN, and A. AMADEI "A Comparison of Techniques for Calculating Protein
Essential Dynamics". JCC Vol. 18, No 2, 169-181 (1997) and I have not access
to your first article from 1993.

  After generation structure by CONCOORD we have two main files needed for
work with g_covar - first - structure.pdb and second - trajectory.xtc. In
trajectory.xtc we have 500 generated by CONCOORD structures each of which
contains same atoms as initial structure in structure.pdb ( e.g. sidechain
atoms, all backbone atoms ).

  First.
  When I use option -ref in g_covar input I give in covar.log "wrote average
structure to eigenvec.trr with t=0" although in manual one of two functions
of -ref option is writing ref structure with t=0 to eigenvec.trr instead of
average when -ref option is used.
  Why in eigenvec.trr last frame has t=499, but not the 500 as in initial
trajectory.xtc file ( data obtained after trjconv program with -sep
option ) - plus original structure with t=-1 and average with t=0 - all is
501, but I think should be 502
( t=-1, t=0, and t= from 1 to 500 - where is structure No 500 ) ?
  Since in chapter 8 said that covariance analysis depends on what structure
was used in analysis - how can I decide what is better - use average ore
reference structure for covariance analysis ? Are here some recipes.

  Second. Most problems I have with understandig g_anaeig program.
  In manual said "When a trajectory is projected on eigenvectors, all
structures are fitted to the structure in the eigenvector file if present,
othrwise to the structure in the structure file". When I use in g_covar same
structures for fitting and analysis I always have initial structure in
eigenvec.trr file with t=-1 ( as described in g_covar manual chapter ). But
when I attempt to use as follows "g_anaeig -v eigenvec.trr -f
trajectory.xts -extr str.ext.pdb" without -s option ( there is reference
structure in eigenvec.trr with t=-1 ) I give fatal error : no topol file.
What is need in this file here ?
 Then could you give me more detailed description of -extr option. It is not
clear how does extreme values calculation perform ( at the ideas level )-
and what are these values. What is function of -max option - what other
extreme values can be obtained with this option when its value is not equal
to zero?
 What functions of -2d and -3d options and in what they differ from -proj
option and for what goals I can use this option ( except, probably, -proj -
I think I understand main function of -proj option - it is needed for next
cosine content calculation with g_analyse to asess are motions described by
obtained eigenvectors not random - am I right in this question ? ) ?
 When I use -filt option I give the same amount of frames as in other
 after g_covar ) trajectory files - ( last number is 499 ). Intuitively I
supposed that after filtration number of frames should be decresed - how
does filtration perform and what results I can obtain with this option?

  Other options as I believe I understand now, except, may be, -inpr
options - how and in what situations its results may I use.

  Third. Most main question - may I and if yes, how may I obtain end
conformations of my original structure projected on eigenvectors and is it
possible to obtain these conformations with the all ( not only C-alpha atoms
that was used in g_covar for analysis ) atoms.

Thank you very much for your attention to my problem.

With my best wishes,
D.Egorov, USMA, 27.12.2002.