Hi,
On Tue, Mar 23, 2021 at 5:51 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> parm .*.prmtop
> trajin ...
> trajin ..
> hbond S1 series out series.dat nointramol image \
> donormask :ACT.N donorhmask :ACT.H \
> acceptormask :TCA.O \
> avgout avg.dat
> #
> hbond S2 series out series2.dat nointramol image \
> donormask :ACT.O donorhmask :ACT.OH \
> acceptormask :TCA.O \
> avgout avg2.dat
> #
> run
> runanalysis lifetime S1[solutehb] out lifetime.dat
> runanalysis lifetime S2[solutehb] out lifetime2.dat
This should work fine. The initial commands prior to 'run' will set up
two separate 'hbond' calculations; generated datasets will be named S1
and S2 respectively. Unlike some other analyses, you have to 'run'
before the 'lifetime' analysis in this case because cpptraj doesn't
know beforehand what hydrogen bonds will be present (although this is
behavior I have some ideas about addressing in the future). As long as
S1 and S2 contain some data, the subsequent 'lifetime' analyses should
run fine.
That said, if you see this is not the case, please let me know so I
can track down and fix any bugs!
-Dan
>
> Best regards
> // Gustaf
>
> > On 22 Mar 2021, at 15:37, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > Hi,
> >
> > You can do all the analysis in one script. However, be aware that
> > certain analyses (like 'rms' with fitting) will alter the coordinates
> > for subsequent analyses. This is in general more important for older
> > versions of cpptraj (< 5.0) but is important to be aware of in all
> > cases.
> >
> > Below is an example of having everything done in one pass, where the
> > commands that do not modify coordinates come first. I'm taking
> > advantage of the fact that you typically want to fit coordinates to a
> > reference structure for 'rmsf' to remove global rotation/translation
> > anyway (which is why 'rmsf' comes after 'rms'); here I'm using the
> > first frame as a reference but you may want to use something else.
> > Also note I'm just doing the 'bare-bones' versions of these commands;
> > you'll want to check the manual for full details (particularly for a
> > more complex command like 'hbond'). Replace <mask> with masks
> > selecting your desired atoms. If you want a better surface area than
> > LCPO, replace 'surf' with 'molsurf' (but be aware it is slower). RoG,
> > HB, LCPO, ToFirst, and Fluct are just used to name the resulting data
> > sets and can be changed to whatever you like. Hope this helps.
> >
> > parm topology.parm7
> > trajin trajectory.nc
> > # Actions that do not modify coordinates
> > rog RoG <mask> out rog.dat
> > hbond HB <mask> out nhbonds.dat avgout hbavg.dat
> > surf LCPO <mask> out lcpo.sa.dat
> > # Best-fit RMSD performed by default
> > rmsd ToFirst first <mask> out rmsd.tofirst.dat
> > rmsf Fluct <mask> out rmsf.dat
> > go
> >
> > Hope this helps,
> >
> > -Dan
> >
> > PS - You may find the analysis tutorials helpful:
> > https://ambermd.org/tutorials/TrajectoryAnalysis.php
> >
> > On Fri, Mar 19, 2021 at 5:25 PM Jatin Kashyap <jk435.njit.edu> wrote:
> >>
> >> Dear AMBER Community,
> >>
> >> I have question about CPPTRAJ. I have to perform RMSD, RMSF, HBOND, SASA,& RoG analysis on around 20 complexes through a shell script based batch job.
> >> For a given complex, do I have to load topology & trajectory file for all of the individual analysis separately or I can just load it once and then perform RMSD, RMSF, HBOND, SASA, & RoG analysis one by one?
> >>
> >> Thank you.
> >>
> >>
> >> ——
> >> Jatin Kashyap
> >> Ph.D. Student
> >> Dr. Dibakar Datta Group
> >> Department of Mechanical and Industrial Engineering
> >> New Jersey Institute of Technology (NJIT)
> >> University Heights
> >> Newark, NJ 07102-1982
> >> Phone- (201)889-5783
> >> Email- jk435.njit.edu
> >>
> >> _______________________________________________
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> >
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Received on Wed Mar 24 2021 - 07:00:03 PDT
