Thanks Daniel
Now it work easily
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
*Md Homaidur Rahman*
PhD Research Scholar
Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036
*Mobile No = +91- 7845991785*
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
On Thu, Jun 25, 2015 at 1:02 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
>
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Received on Wed Jun 24 2015 - 14:30:04 PDT
