On 24/08/2012 4:51 PM, James Starlight wrote:
up :)
It's appeared two additional questions.
1) In addition to the pca's cross-correlation maps I wounder to know
about possibility of calculation of such cross-correlation's from the
trajectories indirectly without calculation of the covariance
matrices.
2) is there any way to calculate degree of fluctuations of side-chains
( degree of torsion's dynamics) from the different trajectories and
to compare it ?
E.g I have one protein in two different (apo and holo) forms. I've
calculated two trajectories for both structures and observed different
degree of dynamics in case of each structure ( e.g fluctuations in
case of apo form were more frequent than in case of liganded form).
IS there any way to direct mesure and comprison of such side-chain's
dynamics for two trajectories?
Yes, but not with GROMACS tools. You can generate a .tpr for use with
that old version of g_covar with an old version of grompp in a manner
similar to the way you generate one now, but there are bunch of details
different. You may not require a .tpr, of course. Look at the file types
for g_covar_mod -s in the output for -h.
Mark
James
2012/8/15, James Starlight <jmsstarli...@gmail.com>:
Dear Gromacs users!
I want to obtain Cross-correlation maps ( for indication of the
cross-correlated fluctuations of the residues).
The example of such maps can be found here
http://pubs.acs.org/doi/abs/10.1021/ja076046a
I found that modificied version of the G_covar from users
contributions can do such things. But because of the older version of
that program (3.3.3) I've obtained the below error using it with 4.5.5
gromacs
Reading file md_GO.tpr, VERSION 4.5.5 (single precision)
-------------------------------------------------------
Program g_covar_mod, VERSION 3.3.3
Source code file: tpxio.c, line: 1192
Fatal error:
reading tpx file (md_GO.tpr) version 73 with version 40 program
-------------------------------------------------------
Is there newest versions of the G_covar for such things or
alternativelly any others ways to calculate such correlations maps ?
Thanks for help
James
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