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
> > > >>
> > > >>
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org
> > > >> http://scanmail.trustwave.com/?c=129&d=odmm0_rRwF4t-ke72pHi04h-Hh
> > > >> nsTJFbwn46wDPTCg&u=http%3a%2f%2flists%2eambermd%2eorg%2fmailman%2
> > > >> flistinfo%2famber
> > > >>
> > > >
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://scanmail.trustwave.com/?c=129&d=odmm0_rRwF4t-ke72pHi04h-HhnsT
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> > > nfo%2famber
> > >
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://scanmail.trustwave.com/?c=129&d=odmm0_rRwF4t-ke72pHi04h-HhnsTJF
> > bwi45xzyEAg&u=http%3a%2f%2fhome%2echpc%2eutah%2eedu%2f%7echeatham%2f
> > (801) 587-9652
> > (801) 585-6208 (Fax)
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> > 2famber
> >
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Received on Mon Jun 23 2014 - 05:00:04 PDT
