Maurício Menegatti Rigo wrote:
Hi,
we are working with a protein-ligand system (MHC + peptide). We have
computed radius of gyration using the following command line:
g_gyrate -f File1.xtc -s File2.tpr -n index.ndx -o GYRATE
* File1: refer to concatenated trajectories of our *protein* plus
*ligand *during 8ns simulation.
We choose the *ligand* group to compute the radius of gyration. My
questions are:
1) Which center of mass GROMACS will set: the center of mass of the
ligand or of the protein?
2) If the center of mass is the protein, all the atoms of the ligand are
used for the radius og gyration calculation?
I see no reason why the receptor's coordinates would be used if you tell
g_gyrate to do its calculation on the peptide ligand. If it did, I would think
that would be a major flaw.
You can convince yourself of this fact by running g_gyrate on a single .gro file
(extracted from the trajectory) that contains only the peptide (so that no other
atoms can possibly be considered), and compare its results to that frame in the
trajectory output.
-Justin
Thanks in advance
--
Maurício Menegatti Rigo
Núcleo de Bioinformática do Laboratório de Imunogenética
Departamento de Genética
Instituto de Biociências
Universidade Federal do Rio Grande do Sul
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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