Hi,
One more thing - note that when you read in the average PDB as a topology,
since it does not contain mass information, the mass-weighted RMSD will be
slightly off from what you would expect (all the masses in that topology
will be set to 1.0). You can get mass information in the reference by
writing out the stripped topology file and reading that back in, like so
(here I am assuming your topology is named 'prmtop'):
parm prmtop
trajin mdcrd1
trajin mdcrd2
# Remove water, output stripped topology as stripped.prmtop
strip :WAT outprefix stripped
# 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 stripped.prmtop
# Load in generated average PDB using stripped topology
reference avg.pdb parm stripped.prmtop
-Dan
PS - In the next release of cpptraj, when you read in a topology that does
not contain mass information it will be set if the elements of the atoms
can be determined.
On Sat, Feb 1, 2014 at 8:42 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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)
>
--
-------------------------
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
