Hi,
On Wed, Jun 24, 2015 at 6:52 AM, MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>
wrote:
> parm 10system/md_out/10SPC.top parmindex 1
>
The 'parmindex' keyword is not part of the 'parm' command (Amber 15 manual,
section 29.6.8).
>
> trajin 0system/md_out/md_file/6_md5_0SPC.crd
> trajin 10system/md_out/md_file/6_md5_10SPC.crd parmindex 1
>
The 'trajin' command does use the 'parmindex' keyword, so this is correct
usage.
>
> strip :SPC
> strip :SPC parmindex 1
>
Again, the 'parmindex' keyword is not part of the 'strip' command (section
29.8.15). All you need is the first 'strip' command, 'strip :SPC', which
will then be applied to all input trajectories.
> trajout ura_0SPC.crd
> trajout ura_10SPC.crd parmindex 1
>
These commands should work.
>
> parmstrip :SPC
> parmstrip :SPC parmindex 1
>
The 'parmstrip' command (section 29.6.11) only needs the index, not the
parmindex command. However, you do not need to run these commands (and
parmwrite). If you want a stripped topology just use the 'outprefix'
keyword of 'strip':
strip :SPC outprefix nowater
So to summarize:
parm 0system/md_out/0SPC.top
parm 10system/md_out/10SPC.top
parm 20system/md_out/20SPC.top
parm 30system/md_out/30SPC.top
parm 40system/md_out/40SPC.top
parm 50system/md_out/50SPC.top
#load trajectory
trajin 0system/md_out/md_file/6_md5_0SPC.crd
trajin 10system/md_out/md_file/6_md5_10SPC.crd parmindex 1
trajin 20system/md_out/md_file/6_md5_20SPC.crd parmindex 2
trajin 30system/md_out/md_file/6_md5_30SPC.crd parmindex 3
trajin 40system/md_out/md_file/6_md5_40SPC.crd parmindex 4
trajin 50system/md_out/md_file/6_md5_50SPC.crd parmindex 5
#Action command
strip :SPC outprefix nowater
trajout ura_0SPC.crd
trajout ura_10SPC.crd parmindex 1
trajout ura_20SPC.crd parmindex 2
trajout ura_30SPC.crd parmindex 3
trajout ura_40SPC.crd parmindex 4
trajout ura_50SPC.crd parmindex 5
Hope this helps,
-Dan
> but it is showing error
>
> CPPTRAJ: Trajectory Analysis. V15.00
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 06/24/15 17:40:01
> | Available memory: 153.504 MB
>
> INPUT: Reading Input from file ptraj4imin5
> [parm 0system/md_out/0SPC.top ]
> Reading '0system/md_out/0SPC.top' as Amber Topology
> [parm 10system/md_out/10SPC.top parmindex 1]
> Reading '10system/md_out/10SPC.top' as Amber Topology
> [parm 20system/md_out/20tmoSPC.top parmindex 2]
> Reading '20system/md_out/20tmoSPC.top' as Amber Topology
> [parm 30system/md_out/30tmoSPC.top parmindex 3]
> Reading '//30system/md_out/30tmoSPC.top' as Amber Topology
> [parm/40system/md_out/40tmoSPC.top parmindex 4]
> Reading '/40system/md_out/40tmoSPC.top' as Amber Topology
> [parm /50system/md_out/50tmoSPC.top parmindex 5]
> Reading '/50system/md_out/50tmoSPC.top' as Amber Topology
> [trajin 0system/md_out/md_file/6_md5_0SPC.crd ]
> Reading '0system/md_out/md_file/6_md5_0SPC.crd' as Amber Trajectory
> [trajin 10system/md_out/md_file/6_md5_10SPC.crd parmindex 1]
> Reading '10system/md_out/md_file/6_md5_10SPC.crd' as Amber Trajectory
> [trajin 20system/md_out/md_file/6_md5_20SPC.crd parmindex 2]
> Reading '20system/md_out/md_file/6_md5_20SPC.crd' as Amber Trajectory
> [trajin 30system/md_out/md_file/6_md5_30SPC.crd parmindex 3]
> Reading '30system/md_out/md_file/6_md5_30SPC.crd' as Amber Trajectory
> [trajin 40system/md_out/md_file/6_md5_40SPC.crd parmindex 4]
> Reading '40system/md_out/md_file/6_md5_40SPC.crd' as Amber Trajectory
> [trajin 50system/md_out/md_file/6_md5_50SPC.crd parmindex 5]
> Reading '50system/md_out/md_file/6_md5_50SPC.crd' as Amber Trajectory
> [strip :SPC ]
> STRIP: Stripping atoms in mask [:SPC]
> [strip :SPC parmindex 1]
> STRIP: Stripping atoms in mask [:SPC]
> Error: [strip] Not all arguments handled: [ parmindex 1 ]
> 1 errors encountered reading input.
> TIME: Total execution time: 0.0355 seconds.
>
>
> As given on Amber 15 Reference Manual for trajin (29.7.1. ) command on page
> 541.
> it will accept both parmindex or tag name during trajectory reading.
> So I tried both in similar way, but in both case I am getting error.
>
> Thank you in advance for your help
> Regards
> Rahman
> _______________________________________________
> 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
Received on Wed Jun 24 2015 - 13:00:02 PDT
