That worked. Thank you very much!
On Tue, Jun 30, 2015 at 9:15 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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?
> > _______________________________________________
> > AMBER mailing list
> > 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jul 01 2015 - 03:00:02 PDT
