On Wed, Jan 21, 2015 at 6:45 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> 1) how to save subset of atoms in the resulted dcd
> for instance I need to save dcd consisted of only protein atoms
> :1-361
> or
> :1-361.CA,N,C -> if I need to save only protein backbone
> or
> :1-361, Mol -> If I need to save protein +ligand
>
> 2) Is it possible to save as the output stripped parm7 file consisted of
> topology of protein + ligand only ?
The answer to both questions is to use the 'strip' command, e.g.
(cpptraj input):
trajin amd_go.nc
# Strip everything but residues 1 to 361, write stripped topology
strip !(:1-361) outprefix strip
trajout stripped.amd_go.dcd
See the manual for complete details on the 'strip' command.
-Dan
>
>
> thanks again for help,
>
> James
>
> 2015-01-20 19:27 GMT+01:00 Daniel Roe <daniel.r.roe.gmail.com>:
>
>> Hi,
>>
>> You're using cpptraj syntax in a lot of these commands. You need to
>> use cpptraj instead of ptraj for this script to work.
>>
>> On Tue, Jan 20, 2015 at 10:53 AM, James Starlight
>> <jmsstarlight.gmail.com> wrote:
>> > trajin amd_go.nc 0 last 1
>>
>> The 'last' keyword for 'trajin' is cpptraj-only. There is no
>> equivalent in ptraj. However, since your offset is '1' you can just
>> use ' trajin amd_go.nc' and all frames will be read.
>>
>> > # fitting to protein
>> > center :1-361 mass origin
>> > image origin center
>>
>> For most cases, 'autoimage' is the recommended command for imaging
>> instead of 'center'/'image' (again, cpptraj only).
>>
>> > trajout md_proc.dcd dcd nobox
>>
>> The 'dcd' keyword is cpptraj-only. For DCD output with ptraj, only the
>> 'charmm' keyword works. If you look at your output it likely says it's
>> defaulting to Amber trajectory format here.
>>
>> My recommendation is to just use cpptraj (from AmberTools 14) since
>> ptraj is no longer actively developed.
>>
>> -Dan
>>
>> >
>> > ! in fact
>> > 1) it produce again full system trajectory without stripping the solvent
>> > 2) broken dcd file (is not recognized by VMD) but there is no problem if
>> I
>> > chose netCDF output again
>> >
>> >
>> > 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
>>
> _______________________________________________
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> 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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Received on Wed Jan 21 2015 - 08:00:08 PST
