Dear All and Dan,
Thank you for the useful suggestions which are now giving the expected
result.
Below is my cpptraj input file in case it is useful to other members on the
list in the near future.
Best wishes and regards.
parm prot-nolig-solv.prmtop
trajin prot-nolig-solv-prod.nc
autoimage
center
strip :LIG parmout prot-nolig-solv.prmtop
outtraj prot-nolig-solv-prod.nc
outtraj prot-nolig-solv-prod.rst7 onlyframes 1
unstrip
strip :WAT,Cl-,Na+,K+,LIG
outtraj prot-nolig-prot.nc
outtraj prot-nolig-prot.rst7 onlyframes 1
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
Please consider the environment before printing this e-mail
On Thu, Apr 7, 2022 at 5:54 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> There are a couple of problems with your script. First, you're using both
> 'parmstrip' and ‘strip’ when you only need the latter. What is happening is
> ‘strip’ only affects the topology for actions, while ‘parmstrip’ affects
> the topology for *everything* (the problem here being that after
> ‘parmstrip’ the topology no longer corresponds to the input trajectory).
> Use the ‘parmout’ or ‘outprefix’ keywords for ‘strip’ if you want a
> stripped topology.
>
> The second issue is you’re using ‘trajout’ (which only outputs after *all*
> actions have been completed) instead of ‘outtraj’ (which respects action
> order). It’s a subtle but important difference.
>
> I highly recommend reading the manual entries for all of these commands for
> more details. In particular the manual entry for ‘unstrip’ has an example
> of what I think you're trying to do.
>
> Hope this helps,
>
> -Dan
>
>
> On Wed, Apr 6, 2022 at 11:46 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
> >
> > 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
> >
> > Please consider the environment before printing this e-mail
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Apr 08 2022 - 00:30:02 PDT
