Hi,
The error messages were stated in the original email. It appears to be some problem with the topology file.
Cpptraj version is 17 and the the input is
parm HEM.prmtop
trajin HEM1.nc 1 -1 1
trajin HEM2.nc 1 -1 1
trajin HEM3.nc 1 -1 1
autoimage
rmsd RMSD :1-578.CA first
trajout HEM_eq.nc
run
rmsd is performed properly
Adding "fixatomorder" before "autoimage" makes it so autoimage is indeed performed but "fixatomorder" modifies the topology file and I can't save it because "parmout" and "outparm" commands (stated in the users manual) aren't working. I would need this modified topology file to visualize the output file propperly.
Martin
________________________________
De: Daniel Roe <daniel.r.roe.gmail.com>
Enviado: martes, 15 de enero de 2019 15:51
Para: AMBER Mailing List
Asunto: Re: [AMBER] Autoimage command not working
Hi,
> Autoimage is not performed. I tried running the "fixatomorder" command and exporting a new topology file but it didn't work.
Can you elaborate here? What version of cpptraj, what is the exact
input you used, and were there any warning/error messages?
-Dan
>
> Any suggestions?
>
> Thanks
>
> Martin
>
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Received on Tue Jan 15 2019 - 12:00:03 PST
