Without knowing the exact error, again I can only speculate. If you
are using a CHAMBER topology these are currently not recognized by
VMD. In order to use it with VMD you need to strip out the CHAMBER
information using the 'nochamber' keyword. Be aware that while this
stripped/nochamber topology will be fine for visualization/analysis,
it should not be used for simulations (since it is now missing
information).
One quick tip: if you're using Amber topologies with VMD a lot, name
them with the '.parm7' extension for automatic recognition.
-Dan
On Tue, Sep 9, 2014 at 12:07 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> Hi Dan,
>
> thank you very much for the help! Indeed in the second case the problem was
> due to the topology
> BTW I've triet to prepare topologies with no box and stripped from water
> taking command sequence from the tutorial- but the resulted topology could
> not recognized by VMD.
>
> parm system.parmtop
> parmstrip :WAT
> parmbox nobox
> parmwrite out stripped.parmtop
>
> Where might be error?
>
> James
>
> 2014-09-08 17:59 GMT+04:00 Daniel Roe <daniel.r.roe.gmail.com>:
>
>> On Mon, Sep 8, 2014 at 2:45 AM, James Starlight <jmsstarlight.gmail.com>
>> wrote:
>> > 1) need to remove periodicity and wrapping from my trajectory
>> >
>> > trajin md.nc 1000 last 5
>> > reference protein.inpcrd
>> > unwrap
>> > center :1-289 mass origin
>> > image origin center
>>
>> This is not a useful command sequence and the exact opposite of what
>> you want. You are unwrapping (i.e. removing imaging) and then
>> re-imaging. If you want to remove wrapping just use 'unwrap'. I
>> strongly recommend you read the manual and become familiar with every
>> command you try to use before you run your calculations.
>>
>> > 2) if I chose possibility to save trajectory after RMSD fitting
>> > trajin md.nc 1000 last 5
>> > reference protein.inpcrd
>> > rms reference :1-289.CA out rmsd.dat
>> > outtraj afterRMSD.nc
>> >
>> > it has produced correct RMSD.dat output but no any processed trajectory
>> > afterRMSD.nc has been appeared in the work dir.
>>
>> If you have multiple topologies specified cpptraj will try to use the
>> first topology for 'trajout'/'outtraj' commands, and if that topology
>> does not match the topology for the input trajectory the output
>> trajectory will not be written. However, without seeing your complete
>> cpptraj output I can only speculate.
>>
>> -Dan
>>
>> >
>> > Thanks for help,
>> >
>> > James
>> > _______________________________________________
>> > AMBER mailing list
>> > 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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> 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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http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 09 2014 - 07:00:02 PDT
