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
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>
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Received on Wed Oct 10 2018 - 05:30:02 PDT
