From: Karol Kaszuba (karol.kaszuba_at_uwm.edu.pl)
Date: Fri Jul 27 2007 - 13:56:22 CDT
Hello,
I would like to report some strange problem.
I performed MD.
I loaded the PSF file.
I loaded the DCD file.
I calculated RMSD for heavy atoms of one SIDECHAIN and I noticed the
following problem:
The RMSD value was irrationally high - reached even 350 A.
The carbon atoms of my sidechain were 300 A away from the protein.
The hydrogen atoms of my sidechain were "in place" (still constituted a
part of the protein).
First I thought that my simulation went abnormally - for example: heavy
atoms of the sidechain "escaped" and remained separated but they didn't -
I was observing them during DCD playing.
It looks like RMSD calculation moves my heavy atoms away from protein.
Furthermore - when I calculated RMSD for whole resid 37 I obtained a
correct rmsd value and the heavy atoms of the sidechain were not moved for
300 A.
I am using the folowing rmsd.tcl script with the VMD for linux 32, version
1.8.5
set outfile [open rmsd_37.dat w]
set nf [molinfo top get numframes]
set frame0 [atomselect top "protein and resid 37 and sidechain and not
hydrogen" frame 0]
set sel [atomselect top "protein and resid 37 and sidechain and not
hydrogen"]
# rmsd calculation loop
for {set i 1 } {$i < $nf } { incr i } {
$sel frame $i
$sel move [measure fit $sel $frame0]
puts $outfile "[measure rmsd $sel $frame0]"
}
close $outfile
I would like to ask if someone know what may cause this problem and how to
omit it?
Thank you in advance,
Regards,
Karol
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:00 CST