Hi,
On Fri, Jan 31, 2014 at 10:25 PM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> I am trying to compute the rmsd to an average pdb - I am using the follow
> input for ptraj as described below - the problem is that the reference does
> not seem to exist for the rmsd calculation:
>
The problem here is that reference isn't being generated until *after* the
run completes since you need to have read through all frames in order to
calculate the average. You can either do two separate ptraj runs, or you
can use cpptraj to do it in one run like so:
trajin mdcrd1
trajin mdcrd2
# Remove water
strip :WAT
# Image to the origin
autoimage origin
# Calculate average structure in PDB format
average avg.pdb
# Run, first pass to strip, image, and create average
run
# Read in average PDB as topology since it was stripped
parm avg.pdb
# Load in generated average PDB using PDB topology
reference avg.pdb parm avg.pdb
# Perform global RMS fit to reference
rms reference mass :1-222
# Get RMSD of res 135 with respect to previous fit
rms reference out PHE_135_rmsd.dat :135 nofit
# Run, second pass to calculate RMSD
run
Note I slightly changed the 'rms' commands: in the first I performed the
global fit to the reference instead of the first frame, and in the second I
calculated RMSD of the residue without fitting (otherwise you've rendered
the previous RMS command useless because of the new fit).
Hope this helps; let me know if you have any questions.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sat Feb 01 2014 - 08:00:08 PST
