This works!
Thanks a lot!
2016-03-01 1:17 GMT+09:00 Daniel Roe <daniel.r.roe.gmail.com>:
> On Mon, Feb 29, 2016 at 9:01 AM, Song-Ho Chong <chong.sookmyung.ac.kr>
> wrote:
> >
> > The first line looks like
> > * GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) VERSION ...
>
> Ah, that's the issue - cpptraj's file autodetection needs to be a bit
> more robust here. If you change either the first '*' or space into any
> other character cpptraj will recognize it correctly. I'll have to fix
> that. Change the '*' to a space and see if that works for you.
>
> -Dan
>
> >
> > 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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> > 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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>
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Received on Mon Feb 29 2016 - 08:30:06 PST
