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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Received on Wed Oct 10 2018 - 03:30:02 PDT
