Dear All,
I want to strip a ligand from topology and trajectory and save new topology
and traj files.
For this I tried parmed and cpptraj but the trajectories and topology are
not compatible, since the topology still contains the ligand.
When I used parmstrip in cpptraj I get the following errors.
Can you please suggest me sequence of commands where I can load parmtop and
traj files, then strip both and write new files to be used for further
analysis?
At last I also want to save only protein trajectories without ligand, water
and ions (thus last 4 lines)
thank you and best regards
My current cpptraj input
-------------------------------
parm prot-lig_out-solv.prmtop
trajin prot-lig_out-solv-prod.nc
autoimage
center
strip :LIG
parmstrip :LIG
parmwrite out prot-nolig_out-solv.prmtop
trajout prot-nolig_out-solv-prod.nc
trajout prot-nolig _out-solv-prod.rst7 onlyframes 1
unstrip
strip :WAT,Cl-,Na+,K+,LIG
trajout prot-nolig_out-prot.nc
trajout prot-nolig_out-prot.rst7 onlyframes 1
-----------------------------------
Error with cpptraj input
-----------------------------
CPPTRAJ: Trajectory Analysis. V4.25.6 (AmberTools V20.00)
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 04/07/22 09:05:48
| Available memory: 262.355 GB
INPUT: Reading input from 'prot-lig_out-cpptraj.in'
[parm prot-lig_out-solv.prmtop]
Reading ' prot-lig_out-solv.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
[trajin prot-lig_out-solv-prod.nc]
Reading ' prot-lig_out-solv-prod.nc' as Amber NetCDF
[autoimage]
AUTOIMAGE: To box center based on center of mass, anchor is first
molecule.
[center]
CENTER: Centering coordinates using geometric center of atoms in mask
(*) to
box center.
[strip :LIG]
STRIP: Stripping atoms in mask [:LIG]
[parmstrip :LIG]
Error: Topology ' prot-lig_out-solv.prmtop' has already been used to set up
trajectory ' prot-lig_out-solv-prod.nc'.
Error: To strip this topology use the 'strip' action.
1 errors encountered reading input.
TIME: Total execution time: 0.4632 seconds.
Error: Error(s) occurred during execution.
Regards,
Dr. Vaibhav A. Dixit,
Asst. Prof., Department of Medicinal Chemistry,
National Institute of Pharmaceutical Education and Research, Guwahati
(NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
781101, Assam, India
Mob. No. +91-7709129400,
Email: vaibhav.niperguwahati.in; vaibhavadixit.gmail.com
https://niperguwahati.ac.in/DOC/profile/dixit.pdf
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
NCBI bibliography:
https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Wed Apr 06 2022 - 21:00:03 PDT
