Thanks for your reply.
> For example,
> >
> > trajin my_file.crd
> > autoimage
> > trajout my_file.pdb pdb
> >
> > identifies the input crd file as "Charmm COR", generates
> > the error message, Error: No atoms in CHARMM COR file,
> > and cpptraj stops the execution.
>
> What does the first line of your trajectory file look like?
>
The first line looks like
* GENERATED BY CHARMM-GUI (
HTTP://WWW.CHARMM-GUI.ORG) VERSION ...
This is because of the way I produced the amber topology file.
(In short, I proceeded as follows.
1. I used input generator of CHARMM-GUI to get charmm scripts for
generating charmm topology file, since I'm not familiar with charmm,
2. I modified the charmm scripts so that I can use modified charmm force
fields,
3. I used chamber to generate amber topology file from charmm topology
file.)
Simulations were done without any problem.
All the analysis with cpptraj works based on restart files.
Also, all the analysis with cpptraj works based on trajectory files
with the modification of cpptraj code that I mentioned.
> To get around this problem, I replaced the following line
> > in TrajectoryFile.cpp
> >
> > { "Charmm COR", 0, 0, Traj_CharmmCor::Alloc },
> >
> > with
> >
> > { "Charmm COR", 0, 0, Traj_AmberCoord:Alloc },
>
> Be aware that modifying the code in this way may prevent updates from
> successfully applying.
>
I agree ... and I want to avoid this if possible.
> > Then, cpptraj works fine.
> > (There was another problem ... I had to manually add
> > parmbox alpha 90 beta 90 gamma 90
> > to use autoimage.)
>
> Your topology/trajectory combination must be very strange to encounter
> these issues. One of the many disadvantages of working with ASCII
> trajectories instead of NetCDF is that since box angles are typically
> not stored in Amber ASCII trajectories, cpptraj is reliant on the box
> information in the Amber topology file. Does your topology not contain
> a '%FLAG BOX_DIMENSIONS' section?
My topology file (generated by chamber as mentioned above)
does not contain a '%FLAG BOX_DIMENSIONS' section.
At the moment, this is not a main issue since I can get around this
with parmbox.
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Received on Mon Feb 29 2016 - 08:30:03 PST
