Hi,
On Sun, Nov 28, 2021 at 10:47 AM Seibold, Steve Allan <stevesei.ku.edu> wrote:
> > trajin HADHR_amber.pdb
> Reading 'HADHR_amber.pdb' as PDB
> Error: PDB HADHR_amber.pdb: No frames read. atom=5265 expected 10544.
> Error: Could not set up 'HADHR_amber.pdb' for reading.
> Error: Could not set up input trajectory 'HADHR_amber.pdb'.
When you load a trajectory into cpptraj, if you don't specify a
topology it will by default try to use the first topology. In this
case your topology (HADHR.prmtop) has more atoms (10544) than the
structure you are loading (HADHR_amber.pdb); I'm guessing this is
because the topology has solvent and the structure does not. You could
just try using the PDBs themselves as topology files:
parm HADHR_amber.pdb
trajin HADHR_amber.pdb
parm HADHN_amber.pdb
reference HADHN_amber.pdb parm HADHN_amber.pdb
You may find the following tutorials useful for understanding how
cpptraj uses topology/trajectory info:
https://ambermd.org/tutorials/analysis/tutorial0/index.php and
https://ambermd.org/tutorials/analysis/tutorial1/index.php. See also
here for useful cpptraj info: https://amberhub.chpc.utah.edu/
Hope this helps,
-Dan
>
> I must be doing something incorrect.
>
> Thanks for your help...
> Steve
>
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Received on Wed Dec 01 2021 - 05:30:02 PST
