Thanks Daniel.
Regards
Kshatresh
On Wed, Oct 10, 2018 at 2:18 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> If you need the topology as well as the coordinates use the ‘parmout’
> keyword for the ‘strip’ command. The ‘strip’ command does not permanently
> alter topologies which is why ‘parmwrite’ is writing the original topology.
>
> -Dan
>
> On Wed, Oct 10, 2018 at 6:29 AM Kshatresh Dutta Dubey <kshatresh.gmail.com
> >
> wrote:
>
> > Dear Users,
> >
> > I need to strip all water residues beyond a certain distance from a
> residue
> > name 0GA and need to regenerate a new prmtop file. I am using cpptraj for
> > this purpose using the following command:
> >
> > parm new-noions.prmtop
> > trajin new-noions.rst
> > reference new-noions.rst
> > strip !(:0GA<:35)
> > parmwrite out strip-wat.prmtop
> > go
> >
> > However, the output prmtop file is not stripped and contains the same
> > number of atoms as the parent prmtop file. The log of the cpptraj run is
> as
> > follows:
> >
> > *PARAMETER FILES (1 total):*
> > * 0: new-noions.prmtop, 88822 atoms, 27304 res, box: Orthogonal, 26772
> mol,
> > 26766 solvent*
> >
> > *INPUT TRAJECTORIES (1 total):*
> > * 0: 'new-noions.rst' is an AMBER restart file with velocity info, Parm
> > new-noions.prmtop (Orthogonal box) (reading 1 of 1)*
> > * Coordinate processing will occur on 1 frames.*
> >
> > *REFERENCE FRAMES (1 total):*
> > * 0: new-noions.rst:1*
> > * Active reference frame for distance-based masks is 'Cpptraj Generated
> > Restart'*
> >
> > *BEGIN TRAJECTORY PROCESSING:*
> > *.....................................................*
> > *ACTION SETUP FOR PARM 'new-noions.prmtop' (1 actions):*
> > * 0: [strip !(:0GA<:35)]*
> > * Stripping 51789 atoms.*
> > * Stripped topology: 37033 atoms, 10041 res, box: Orthogonal, 9509 mol,
> > 9503 solvent*
> > *----- new-noions.rst (1-1, 1) -----*
> > *100% Complete.*
> >
> > *Read 1 frames and processed 1 frames.*
> > *TIME: Avg. throughput= 19.3211 frames / second.*
> >
> > *ACTION OUTPUT:*
> > *TIME: Analyses took 0.0000 seconds.*
> >
> > *RUN TIMING:*
> > *TIME: Init : 0.0001 s ( 0.18%)*
> > *TIME: Trajectory Process : 0.0518 s ( 97.70%)*
> > *TIME: Action Post : 0.0000 s ( 0.00%)*
> > *TIME: Analysis : 0.0000 s ( 0.00%)*
> > *TIME: Data File Write : 0.0000 s ( 0.00%)*
> > *TIME: Other : 0.0011 s ( 0.02%)*
> > *TIME: Run Total 0.0530 s*
> > *---------- RUN END ---------------------------------------------------*
> >
> > I will be thankful if someone could suggest me for the proper way to get
> > the stripped topology.
> >
> > Thanks and best regards
> > Kshatresh
> >
> >
> >
> > --
> > With best regards
> >
> >
> ************************************************************************************************
> > Dr. Kshatresh Dutta Dubey
> > Researcher,
> > Institute of Cell and Molecular Biology
> > Uppsala University
> > Uppsala, Sweden
> > _______________________________________________
> > 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
>
--
With best regards
************************************************************************************************
Dr. Kshatresh Dutta Dubey
Researcher,
Institute of Cell and Molecular Biology
Uppsala University
Uppsala, Sweden
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Received on Wed Oct 10 2018 - 09:00:03 PDT
