ps. there is also an atom misbalance error:
No frames read. atom=35369 expected 35404.
On Tue, Jun 30, 2015 at 8:42 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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Received on Tue Jun 30 2015 - 13:00:03 PDT
