Re: RMSD and merging trajectories

From: Axel Kohlmeyer (
Date: Sat Jan 24 2009 - 19:18:51 CST

On Sat, 24 Jan 2009, Falgun Shah wrote:

FS> Dear sir

FS> I am trying to calculate per residue rmsd. The protein i am using has 3
FS> residues with negative indexes. so when i execute "rmsd_residue_over_time
FS> top $sel_resid" i am getting following error: atomselect: cannot parse
FS> selection text: protein and resid -3 and noh

this is a VMD question and should therefore be posted on
the VMD mailing list.

as for your problem. have a closer look at the atomselect syntax
and particular the quoting rules. using resid '-3' or resid "-3"
should work just fine.

FS> i have 3 segment in the pdb file. Please let me know how to deal with the
FS> issues. Also, i wanted to know how to merge trajectories from previous run
FS> for RMSD or energy analysis (trajectories generated during different time
FS> interval).

what do you mean by "during different time interval"?

first of all, you can always analyse the trajectory piece by piece
and then then merge the resulting data sets. that can actually be
much more convenient. for merging trajectory files there is catdcd
or you can just use the "Load Data into Molcule..." dialog in VMD.
again, have a look at the user's guide.


FS> Regards

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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