Dear Amber users!
For this example in my work dir I have 6 folders named sim_1, sim_2 ...
sim_6 consisted of all required input files including sh scripts which run
MD for each system. I need an idea for some shell main script which will
run several md jobs at the same time. For instance totally I need run 6 md
jobs (just run six simulation_№(1-6).sh launch files in each sim folder).
Because my workstation has 2 GPUs I have to run only 2 simulations at same
time repeating each circle 3 times (2sims*3repeations like in GYM when we
do lifting :-) )
Below I can see my suggestion about such main script. Using csh (or bash) I
can use some loops e.g foreach or while in csh
foreach i (1 2 3 4 5 6)
cd ./simulation_$i
sh simulation_$1.sh
cd ..
end
Hovewer this algoritm will run next (i+1) simulation (.sh file) only in
case when previous (i) have been finished. How should I modify my script
to make 2 simulations in each for repetition providing also in each
simulation path to the specified GPU ( I guess in csh it could be done by
means of adding "set env CUDA_VISIBLE_DEVICE 0,1" in the foreach loop of my
main script ).
Thanks for help,
James
2014-06-23 18:30 GMT+04:00 Parker de Waal <Parker.deWaal.vai.org>:
> HI James,
>
> I don't believe this is a de-novo approach, rather an in-silico
> introduction of backbone dependent rotomters. When introducing point
> mutations the structure of the protein will not be altered, simply a
> residue will be replaced with another.
>
> To your second point, yes you could do that. You could simply loop over
> the pdb file, and subsiquent mutant pdbs until all the desired mutations
> are applied. Ex:
> BASEPDB -> 1, LEU -> 1LEUPDB
> 1LEUPDB -> 2, ASN -> 2ASNPDB
> etc etc.
>
> I'm sure there are better ways to do this, however this would be quite
> simple to write. Good luck.
>
> Best,
> Parker
> ________________________________________
> From: James Starlight [jmsstarlight.gmail.com]
> Sent: Monday, June 23, 2014 7:48 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] bash scripting for MD tasks
>
> Thanks for suggestions!
>
> In fact this script uses input WT pdb as the template + list of mutation in
> mutate.dat for de-novo modelling of the mutated protein using modeller,
> doesn't it? If yes my questions: 1) How the conformation of flexible parts
> of the mutated protein (e.g loops) be perturbed (in comparison to the WT
> model) in case when mutations will be introduced in this regions after such
> modelling ?
> 2) Some trivial question but should be specified. Might such python script
> used with multiple mutations.dat files to produce several mutants from 1 WT
> model an once (e.g by means of new looping script using python
> mutate_model.py, dat files for each mutant and 1 WT pdb as the inputs) ?
>
> TFH,
>
>
> James
>
>
> 2014-06-22 18:07 GMT+04:00 Parker de Waal <Parker.deWaal.vai.org>:
>
> > while read mutations -r -d ',' mutLoc aminoAcid ; do
> > python mutate_model.py PDB_NAME $mutLoc $aminoAcid A > $mutLoc.log
> > done <mutations.dat
> >
> > Fixed line break.
> > -----Original Message-----
> > From: Parker de Waal [mailto:Parker.deWaal.vai.org]
> > Sent: Sunday, June 22, 2014 10:04 AM
> > To: 'AMBER Mailing List'
> > Subject: Re: [AMBER] bash scripting for MD tasks
> >
> > Hi James,
> >
> > I would highly recommend a quick google search for 'mutate pdb residue'.
> > You'll find the second or third link provides a nice python script to
> > interface with Modeller which you could easily automate to introduce
> > hundreds of mutations.
> >
> > Example:
> > #!/bin/bash
> > cat > mutations.dat <<'EOF'
> > 1, LEU
> > 2, ASP
> > 3, ASN
> > 4, LYS
> > EOF
> >
> > while read mutations -r -d ',' mutLoc aminoAcid ; do
> > python mutate_model.py PDB_NAME $mutLoc $aminoAcid A > $mutLoc.log done
> > <mutations.dat
> >
> > Please note I did not test this script, however it should work.
> >
> > Parker
> >
> > -----Original Message-----
> > From: James Starlight [mailto:jmsstarlight.gmail.com]
> > Sent: Sunday, June 22, 2014 9:25 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] bash scripting for MD tasks
> >
> > Thanks Dan,
> >
> > One of my task consits of the quick introduction of the point mutations
> to
> > the given PDB of membrane receptor and further creation of the models of
> > the mutated protein by the tleap. Assuming I can easily make script for
> the
> > second part of this workflow having as the input mutated pdb and solvated
> > membran in merged pdb I dont absolutely know how I could make quickly
> > mutations in the receptor avoiding of the usage of any GUI-programs like
> > CHIMERA.
> >
> > I'll be thankful for any proposed solutions.
> >
> > James
> >
> >
> > 2014-06-20 18:47 GMT+04:00 Daniel Roe <daniel.r.roe.gmail.com>:
> >
> > > See the supporting info in this publication:
> > > http://scanmail.trustwave.com/?c=129&d=oNmm09uxxQhwv7nR-AzXvp7JpjTPPzP
> > > RoPkyOe7veg&u=http%3a%2f%2fpubs%2eacs%2eorg%2fdoi%2fabs%2f10%2e1021%2f
> > > jp4125099
> > >
> > > -Dan
> > >
> > >
> > > On Fri, Jun 20, 2014 at 8:25 AM, James Starlight
> > > <jmsstarlight.gmail.com>
> > > wrote:
> > >
> > > > One question about possible algorithm for quick checking of the
> > > convergence
> > > > of my trajectory (ies).
> > > > For instance I'd like to write some simple script having as the
> > > > input several trajectories of the same system with different length
> > > > to check
> > > (for
> > > > instance by means of principal mode analysis or another not very
> > > expensive
> > > > method) in what case my system have been converged fully. Are there
> > > > any examples of such scripts or ready workflows?
> > > >
> > > > James
> > > >
> > > >
> > > > 2014-06-19 17:52 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> > > >
> > > > > Thanks, Jason!
> > > > >
> > > > > It's very useful advises and you've made very great script library!
> > > I'll
> > > > > try to follow your basic ideas during my own studies.
> > > > >
> > > > > James
> > > > >
> > > > >
> > > > > 2014-06-17 23:25 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> > > > >
> > > > > On Tue, 2014-06-17 at 22:16 +0400, James Starlight wrote:
> > > > >> > Hi Dan,
> > > > >> >
> > > > >> >
> > > > >> > many thanks for the bash guide- I've found it very useful. In
> > > general
> > > > >> I'd
> > > > >> > like to look at some basic bash script examples suitable for
> > > > >> > typical
> > > > md
> > > > >> > jobs dealing with the running of many of simulation on clusters
> > > > because
> > > > >> the
> > > > >> > most complicated examples like replica exchange simulation have
> > > > already
> > > > >> > been present in the amber tutorials.
> > > > >>
> > > > >> You've gotten the most helpful responses you can possibly get
> > > > >> about
> > > your
> > > > >> question so far, so I won't belabor the points others have made.
> > > > >> I'll relay my own opinions on the topic, though.
> > > > >>
> > > > >> Scripting is, at its core, simply a tool we (as computational
> > > > >> scientists) use to increase our efficiency and productivity. For
> > > > >> example, high-throughput work like screening a database of
> > > > >> millions of compounds cannot be done unless "scripted."
> > > > >>
> > > > >> When you are designing an experiment or calculation you want to
> > > perform,
> > > > >> you have a list of tasks you need to get done. Designing a
> > > > >> script to carry out these tasks requires you to divide your
> > > > >> problem up into simpler chunks that can be easily represented
> > > > >> with common logic structures in programming/scripting, like loops
> > > > >> and simple
> > > conditionals.
> > > > >> Writing the script is easy -- if you don't know the syntax of
> > > > >> doing something like looping over a list, you can google your
> > > > >> question and
> > > see
> > > > >> that it has most likely been asked and answered several times on
> > > > >> StackOverflow before.
> > > > >>
> > > > >> _Designing_ the script is the real challenge (it is an art). It
> > > > >> is
> > > not
> > > > >> something easily taught in a tutorial (nor is there any one
> "right"
> > > way
> > > > >> to do it). You can use the existing tutorials, and the scripts
> > > written
> > > > >> therein, to try and reverse-engineer the design and try to
> > > > >> understand the thought process that led the tutorial authors to
> > > > >> write it that
> > > way.
> > > > >> Then if you're ambitious, try improving it.
> > > > >>
> > > > >> When you are doing your own project, focus on carrying out your
> > > > >> experiment. If you come up to a part that is particularly
> > > > >> repetitive
> > > or
> > > > >> something that fits conceptually into a scripting or programming
> > > > >> paradigm, write a script to handle that part (Googling your
> > > > >> question when you don't know how to do something). The more you
> > > > >> do this, the better you will get at scripting and the more you
> > > > >> will be able to automate your workflows.
> > > > >>
> > > > >> If you find yourself doing the same thing over and over for
> > > > >> different projects (like imaging a trajectory or RMS-fitting your
> > > > >> system with cpptraj or computing a distance and plotting the
> > > > >> result), try to
> > > write a
> > > > >> script to automate that task. As your experience in the field
> > > > >> grows,
> > > so
> > > > >> too will your library of scripts you find useful and your
> > > > >> scripting ability overall. Mine is here:
> > > > >> http://scanmail.trustwave.com/?c=129&d=oNmm09uxxQhwv7nR-AzXvp7Jpj
> > > > >> TPPzPRoPlia-rteg&u=https%3a%2f%2fgithub%2ecom%2fswails%2fjmsscrip
> > > > >> ts%2f
> > > > and
> > > > >> a trained eye can clearly see which ones I wrote when I was
> > > experienced
> > > > >> and which I didn't.
> > > > >>
> > > > >> 6 years ago, I had never used Unix before. I was decent at
> > > > >> scripting within a few months and quite strong within a year or
> > > > >> two -- all following the above advice. That which is
> > > > >> self-learned is learned the best (and is remembered the longest).
> > > > >>
> > > > >> Always rambling,
> > > > >> Jason
> > > > >>
> > > > >> --
> > > > >> Jason M. Swails
> > > > >> BioMaPS,
> > > > >> Rutgers University
> > > > >> Postdoctoral Researcher
> > > > >>
> > > > >>
> > > > >> _______________________________________________
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> > > > >>
> > > > >
> > > > >
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> > >
> > >
> > >
> > > --
> > > -------------------------
> > > Daniel R. Roe, PhD
> > > Department of Medicinal Chemistry
> > > University of Utah
> > > 30 South 2000 East, Room 201
> > > Salt Lake City, UT 84112-5820
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Received on Mon Jul 21 2014 - 05:00:02 PDT
