Hi Kevin,
Thanks again for your detailed response. I'm not very interested yet in
what the ions are doing; they're just their for experimental conditions and
to neutralize my system. I was planning on having a production run between
50ns and 100ns, so initially I might just treat this run as an ion
equilibration, depending on if I see any interesting ion behaviors towards
the end of a few of these trajectories.
Finally, I just wanted to add a step that I'd missed in my previous
protocol:
1. Solvating my molecule
2. Using Dr. Cheatham's molarity.perl script to calculate the number of
ions needed for a certain concentration
3. Adding net neutralizing ions (Cl in my case) (using addIons in my case
-- this may change for users with crystal waters)
4. Adding ions one molecule (of KCl in my case) at a time. This results in
non-crystallized KCl around my protein. (again using addIons in my case)
5. Using the "randomizeions" command in ptraj to result in a more random
distribution of the ions throughout the water box.
6. Using the setbox command in leap to re-add the box parameters, which
ptraj takes out.
Thank you all again so much for your help, and have a great weekend!
Kamali
2012/7/5 Kevin Hauser <84hauser.gmail.com>
> Hi, Kamali,
>
>
> Glad to hear leap is now behaving itself.
>
> On Thu, Jul 5, 2012 at 10:41 AM, Kamali Sripathi <ksripath.umich.edu>
> wrote:
> > Hi Kevin,
> >
> > Thank you very much for your long and detailed response! I've been trying
> > out some suggestions from you and from others in this thread. I've found
> > that what works best for me (for future reference of others with similar
> > problems) is
> >
> > 1. Solvating my molecule
> > 2. Using Dr. Cheatham's molarity.perl script to calculate the number of
> > ions needed for a certain concentration
> > 3. Adding net neutralizing ions (Cl in my case)
> > 4. Adding ions one molecule (of KCl in my case) at a time. This results
> in
> > non-crystallized KCl around my protein.
>
> Make sure the ions don't replace any crystal waters, if you have them...
>
> > 5. Using the "randomizeions" command in ptraj to result in a more random
> > distribution of the ions throughout the water box.
> >
> > Because of the size of my system, I've had to write a script containing
> all
> > of the above leap commands and one containing the ptraj command, and
> submit
> > these as two separate cluster jobs. However, others with smaller systems
> > probably won't have to do that.
> >
> > Robin's AddIonsRand command in Leap does seem faster; however, I haven't
> > installed the latest version of AmberTools yet, so I haven't tried it
> out.
> >
> > I did have a question, though: is it possible to have ions that are too
> > well-distributed throughout the water box?
>
> Excellent question that depends entirely your goals and hypotheses. Is
> it your goal to figure out what the ions are doing, or do you just
> want to include explicit ions to model experimental conditions? Note
> that PME is pretty powerful..
>
> I ask this mainly because I'm
> > concerned, with the use of the randomizeions command, that I will move
> the
> > neutralizing chloride ions too far away from the most electrostatically
> > favorable locations. Conversely, I know that I can specify residue
> numbers
> > in ptraj, and simply leave out the residue numbers for the neutralizing
> > chloride ions, but I feel that this might result in artificially
> > long-residence chloride ions near certain areas of the protein. Is it bad
> > practice to randomize ions using ptraj, and then hope that equilibration
> is
> > long enough (550 ps in my case) to allow the ions to find or return to
> the
> > most electrostatically favorable locations?
>
> Again, depends on what you want to learn. 550ps is a bit on the short
> side compared to our usual 1000ps equilibration, which is still on the
> short side of ion equilibration times.
>
> I haven't found any threads in
> > the AMBER mailing list archive specifically addressing this question, but
> > please do let me know if any exist, and also if there are publications
> that
> > would be particularly helpful.
>
> I've read that equilibration times for ions can range from ~50 ns to
> 100s of ns. This is different from experimental structure
> equilibration. This just means that you need 50-100s ns of straight MD
> for the ion grids to converge. The Amber Masters may have more learned
> recommendations to make, but I would recommend equilibrating a couple
> systems to generate independent runs (using the prmtop/crd you just
> built): for example your first step in equilibration is 10k steps of
> minimization. The second step would be to introduce some temperature -
> since this is the first step of MD, you can set ig differently
> (explicitly, for each run set this number to a different value, see
> Amber manual...) and therefore generate "independent trajectories".
>
> But as a disclosure, I don't know your system. Each system is
> different and you will have to read a lot of papers to figure out what
> you need to do. You'll most likely have to experiment. (I'm a DNA guy,
> so Cheatham, Case, Orozco, Sponer, Lavery, Beveridge and oh so many
> more 8^)
>
> "If we knew what we were looking for, it wouldn't be called
> _re_search" - Einstein...
>
> >
> > Thank you all very much, and have a great weekend,
> >
> > Kamali
> >
> > 2012/6/22 Kevin Hauser <84hauser.gmail.com>
> >
> >> Hi, Kamali,
> >>
> >>
> >> I haven't tried Dan's or Robin's method but will likely do so soon
> enough.
> >>
> >> I'm not sure why you're using addions2 or why you're adding ions before
> >> solvating the system. My responses, inserted below, assume all you care
> >> about is that you end up with 0.15 M salt and that the initial
> >> configuration of ions is evenly distributed around your system.
> >>
> >> On Fri, Jun 22, 2012 at 2:51 PM, Kamali Sripathi <ksripath.umich.edu>
> >> wrote:
> >>
> >> > Thanks a lot, Robin; I'll give that a try.
> >> >
> >> > Dr. Cheatham, I actually had a follow-up question for you. I've been
> >> using
> >> > your molarity.perl script to calculate the number of ions I'd need
> for a
> >> > certain box size. My problem is that I solvate after adding ions, so
> that
> >> > the box size is always a bit off. For example, I calculated by hand
> >> (before
> >> > I had found the script) that I needed 111 molecules of KCl to reach a
> >> > concentration of 0.15 M. Just to double-check, I plugged in my box
> >> > dimensions after adding these 111 molecules and solvated my system.
> The
> >> > script then told me that I'd need 128 molecules. I started over, and
> >> added
> >> > 128 molecules to my system and solvated. As another double-check, I
> >> plugged
> >> > in the parameters of this box into the molarity.perl script, which
> told
> >> me
> >> > that I now needed 131 molecules. I know the best way to do this would
> be
> >> to
> >> > solvate my system and use addions2 to add molecules after solvation.
> >> > However (as I think I mentioned), I tried this, and my system is so
> big
> >> > that Leap crashed.
> >>
> >>
> >> Did you try adding ions one pair at a time (as Tom suggested)? Did you
> try
> >> using addions instead of addions2 (see AmberTools15 manual page 52) or
> >> Robin's AddIonsRand?
> >>
> >>
> >> > Do you have any suggestions for how I might get my
> >> > desired salt concentration?
> >> >
> >>
> >> In case a future Google search is made that this thread comes up on:
> >>
> >> *Step 1.* Run leap with the final solvent size you want. Do not add any
> >> ions yet. Just solvent.
> >> *Step 2.* Use *tail* (see bash, please) to get the box information (last
> >> line of *crd file), e.g.,
> >> 96.1984 97.1984 98.1984 109.4712190 109.4712190 109.4712190
> >>
> >> *Step 3.* Copy and paste the box information into Professor Tom's script
> >> appropriately, e.g.,
> >> ./Tom.pl *0.15* 96.1984 97.1984 98.1984 109.4712190 109.4712190
> 109.4712190
> >>
> >> Resulting in,
> >>
> >> MOLARITY = 0.150
> >> Box size = 96.198 97.198 98.198 109.471 109.471 109.471
> >> Volume = 706821.110
> >>
> >> 63.847 molecules are necessary to make a molarity of 0.15M
> >>
> >> *Step 4. Bash a bit,*
> >>
> >> #!/bin/bash
> >> for i in $(seq 1 64); do
> >> echo addions mol K+ 1 Cl- 1
> >> done
> >>
> >> Resulting in 64 lines of,
> >> addions mol K+ 1 Cl- 1
> >>
> >>
> >> *Step 4.1* Add the 64 lines of "addions mol K+ 1 Cl-" to the leap
> >> script *_*after
> >> solvate line_**, e.g.
> >>
> >> #!/bin/bash
> >> #leap stuff here
> >> mol = loadpdb ./solute.pdb
> >> ...
> >> *solvateOCT mol TIP3PBOX 84*
> >> *addions mol K+ 0*
> >> *addions mol K+ 1 Cl- 1*
> >> ...
> >> ...
> >>
> >> *Step 4.2. Run your leap script like so,*
> >> ./leap_script.sh .& leap_script.out-2012-06.22.log &
> >> then you can
> >> grep "Done adding ions" leap_script.out-2012-06.22.log|wc
> >> to see how far along leap is, if you're impatient and in need of instant
> >> gratification.
> >>
> >> *Step 5. Randomize your ions. *This step ought to address your second
> issue
> >> of ions hanging around some domains and not others.
> >>
> >> ptraj prmtop << EOF
> >> trajin inpcrd
> >> trajout inpcrd.rand restart
> >>
> >> prnlev 3
> >>
> >> randomizeions :K+,Cl- around :$X by Y overlap Z noimage
> >> EOF
> >>
> >> Where X= the resnames of all the residues in the solute, to suit; Y and
> Z
> >> can be found in the literature. Professor Tom has some very detailed
> >> Methods sections 8^)
> >>
> >> Things to consider: adding net neutralizing ions; box size after
> >> equilibration; whether you really want ions to be randomized or you want
> >> them to go where the electrostatics are good. For this you may want to
> look
> >> into Dan's work. Also, Robin's method is probably not only easier but
> >> faster than what I've outlined here...
> >>
> >>
> >> HTH,
> >> Kevin
> >>
> >> --
> >> -- - -
> >> HK
> >>
> >>
> >>
> -----------------------------------------------------------------------------
> >> Kevin Hauser
> >> The Louis and Beatrice Laufer
> >> Center for Physical and Quantitative Biology
> >> at Stony Brook University
> >>
> >> National Institutes of Health,
> >> Chemical Biology Interface Training Program Fellow
> >>
> >> The Department of Chemistry
> >> Stony Brook University
> >> Stony Brook, New York 11794
> >>
> >> Phone: (561) 635.1848
> >> Email: 84hauser.gmail.com
> >>
> >>
> -----------------------------------------------------------------------------
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -- - -
> HK
>
>
> -----------------------------------------------------------------------------
> Kevin Hauser
> The Louis and Beatrice Laufer
> Center for Physical and Quantitative Biology
> at Stony Brook University
>
> National Institutes of Health,
> Chemical Biology Interface Training Program Fellow
>
> The Department of Chemistry
> Stony Brook University
> Stony Brook, New York 11794
>
> Phone: (561) 635.1848
> Email: 84hauser.gmail.com
>
> -----------------------------------------------------------------------------
>
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>
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>
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Received on Fri Jul 06 2012 - 07:30:02 PDT
