Would one need to separate datasets when performing lifetime analyses say during a hydrogen bond analyses session?
Let's say I am running the analyses below:
parm .*.prmtop
trajin ...
trajin ..
hbond S1 series out series.dat nointramol image \
donormask :ACT.N donorhmask :ACT.H \
acceptormask :TCA.O \
avgout avg.dat
run
runanalysis lifetime S1[solutehb] out lifetime.dat
Can you set up this to run several analyses whit the trajectory data already loaded? I remember trying to get this to work several years ago without success. The avgout I think I remember working though the lifetime never ran right. If possible, how would one set this up?
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
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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Mar 23 2021 - 03:00:02 PDT
