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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--
-------------------------
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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Received on Mon Feb 29 2016 - 08:30:04 PST
