Hi,
First, use cpptraj from AmberTools 15. That should get around the EPW
warning (earlier versions of cpptraj didn't know what to make of extra
points).
> rmsd fakefit :1-89.N,CA,C ref [fit] :1-159.N,CA,C mass out testFit.dat
RMSD only makes sense when there is a 1 to 1 correspondence between target
and reference atoms - this means that your target mask (the first one)
needs to be selecting the same number of atoms (and in the same order) as
in your reference mask. This is clearly not going to happen with your
current input since you have 89 residues in the first mask and 159 in the
second.
> reference jo_proteinOnly.pdb [noIons] [fit]
You're missing the 'parm' keyword before "[noions]".
Hope this helps,
-Dan
On Tue, Jun 30, 2015 at 1:42 PM, George Green <soyo.green.gmail.com> wrote:
> Hi,
>
> I'm using ambertools 13 and I have a solvated (TIP4P) trajectory and the
> topology files used to create it.
>
> I created an average pdb structure of just the protein atoms. i.e. no
> solvent or ions, then I added waters from the original solvated trajectory
> to the end of the pdb using cat. As I would like to rms fit the protein in
> the trajectory and output pdbs with protein and water molecules only. I
> tried:
>
> #############################
> parm jo_solv.parm [full]
> trajin traj1.crd 1 1 1 [full]
> autoimage
> strip :K+
> parm jo_solv_noIons.parm [noIons]
> reference jo_proteinOnly.pdb [noIons] [fit]
> rmsd fakefit :1-89.N,CA,C ref [fit] :1-159.N,CA,C mass out testFit.dat
> trajout Jo_noIons.pdb PDB multi nobox
> EOF
> #################################
>
> I don't think this is the correct way to do it and I get the following
> error:
>
> "Warning: Could not determine atomic number from name [EPW ]"
>
> Could anyone please help me as to the correct way to do this?
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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 Tue Jun 30 2015 - 13:30:02 PDT
