Anupam Nath Jha wrote:
Anupam Nath Jha wrote:
Dear all
I made an index file with 4 different groups for 4 different chains (since my
protein is a tetramer) and then run
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
to get the rmsd between two different monomers from the same structure,
it asked me two different groups and I gave 0 and 1.
The output file is like this
# g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New
#
# g_rms is part of G R O M A C S:
#
# Grunge ROck MAChoS
#
@ title "RMSD"
@ xaxis label "Time (ps)"
@ yaxis label "RMSD (nm)"
@TYPE xy
@ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1"
0.0000000 0.0000001
In the command you've given (with the same file for -s and -f), you're computing
the RMSD at time zero, after fitting to the structure at time zero, so the RMSD
must be zero.
but I am giving different groups (as chains). I am trying to get RMSD between
two monomers in same structure so what's wrong in that....
It doesn't matter. The structure for calculation (-f) and the reference
structure (-s) are identical, so the RMSD has to be zero, regardless of the
fitting group and calculation groups chosen.
-Justin
-
anupam
so the rmsd = 0.0000001
whereas when I use online server it gives me 1.4.
so what am I doing wrong?
Then whatever you're giving the online server is different. The Gromacs
calculation seems to be correct.
-Justin
regrads
anupam
--
========================================
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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========================================
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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