On Wed, Jul 12, 2017 at 5:54 PM, Guqin Shi <shi.293.osu.edu> wrote:
> Hi Bill,
>
> Thanks for your suggestion on this problem. Dan helped add a new option and
> seemingly solved the problem. (I am writing this email and saw your new
> reply just came in.)
>
> But I did go to check the "pytraj" and I am glad I did so. Previously I
> used cpptraj to get results and write separate python script to process or
> plot the data; but with pytraj it seems two steps could be merged into one.
> Although I didn't utilize pytraj to solve this problem but it's good to
> know it.
shameless ad: process, plot and visualization,
https://github.com/arose/nglview/blob/master/README.md
Hai
>
> As for your previous suggestion on image minimizer, I kinda get your idea.
> Because while Dan was developing the new option, I was using topotools in
> vmd to write protein coordinates from adjacent cells and picked out an
> intact hexamer manually. This is basically (from my understanding...) what
> you were mentioning: get translated images/coordinates and the molecules
> with the closest distance should theoretically be in the "correct"
> complex... But I don't know for this method, how general it could be and
> how efficient it will be (considering the translation have to be done on
> all axes and iterations will be done on all mols/atoms...) I have no
> experience or idea. But I would love to follow up with updates if future
> cpptraj would have such changes.
>
> Best,
> Guqin
>
> On Wed, Jul 12, 2017 at 5:37 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> I still wonder if my idea would be a more general solution, requiring no
>> thought on the user's part.
>>
>> Bill
>>
>>
>> On 7/12/17 2:34 PM, Guqin Shi wrote:
>> > Hi Dan,
>> >
>> > I want to let you know that I have tested the new option for my latest
>> > trajectories. It works very well so far.
>> > The default "autoimage" worked well until 86 ns that conventional way
>> > couldn't work anymore in my case. Then "autoimage" with "moveanchor" were
>> > performed on the following trajectories and so far so good. However, my
>> > simulation is still ongoing. So I will keep testing and report back until
>> > my simulation is done.
>> >
>> > As to the cpptraj tests, "make check" showed that all tests are passed.
>> So
>> > at least nothing I need to worry for now...
>> >
>> >
>> > Thanks a lot for your time and help! I am glad that my special system
>> help
>> > raise a new option...
>> >
>> > Best,
>> > Guqin
>> >
>> > On Wed, Jul 12, 2017 at 10:39 AM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>> >
>> >> Hi,
>> >>
>> >> On Wed, Jul 12, 2017 at 10:32 AM, Guqin Shi <shi.293.osu.edu> wrote:
>> >>> I have multiple production run trajectories which have similar
>> problems.
>> >> I
>> >>> will test them one by one to see how things going. It might take a
>> >> while. I
>> >>> will report back hopefully by tomorrow.
>> >> Great - all feedback is appreciated!
>> >>
>> >>> When I installed cpptraj, there were some warnings. One of them is
>> >>> "Compilation with Sander API failed: (during ./configure). Others are
>> >> This is because your Amber installation is from Amber 14 and the
>> >> sander API has changed since then. Cpptraj's configure detects this
>> >> and disables the sander interface accordingly.
>> >>
>> >>> function warnings such as "unused variable" or "uninitialized" (during
>> >>> "make install"). I attached a file containing these warning messages. I
>> >> These warnings have to do with the 'readline' and 'xdr' libraries and
>> >> can be safely ignored. The real check is to 'make check' in
>> >> $CPPTRAJHOME or 'make test.all' in $CPPTRAJHOME/test.
>> >>
>> >> Hope this helps,
>> >>
>> >> -Dan
>> >>
>> >>> think the latter should be ok. As to the failure with sander API, is
>> this
>> >>> something I need to worry about considering future usage...?
>> >>>
>> >>>
>> >>> Thanks a lot for the help! Great start for today's work!!
>> >>> -Guqin
>> >>>
>> >>> On Wed, Jul 12, 2017 at 10:03 AM, Daniel Roe <daniel.r.roe.gmail.com>
>> >> wrote:
>> >>>> On Wed, Jul 12, 2017 at 9:55 AM, Guqin Shi <shi.293.osu.edu> wrote:
>> >>>>> Or maybe I can replace these two files under my current
>> >>>>> $AMBERHOME/AmberTools/src/cpptraj/src directory..?
>> >>>> This may not work. The GitHub version of cpptraj tends to diverge from
>> >>>> the AmberTools release pretty quickly. This can also mess up future
>> >>>> AmberTools updates. Just stick with the separate install for now.
>> >>>>
>> >>>> -Dan
>> >>>>
>> >>>>> Thanks,
>> >>>>> Guqin
>> >>>>>
>> >>>>> On Wed, Jul 12, 2017 at 8:07 AM, Daniel Roe <daniel.r.roe.gmail.com>
>> >>>> wrote:
>> >>>>>> Hi,
>> >>>>>>
>> >>>>>> The new option is live: https://github.com/Amber-MD/
>> cpptraj/pull/515
>> >>>>>>
>> >>>>>> Just try adding the 'moveanchor' option to your 'autoimage' command.
>> >>>>>> It worked for the frames that you sent me. What it does is that when
>> >>>>>> imaging 'fixed' molecules it uses the previous molecule as the
>> anchor
>> >>>>>> point (the first fixed molecule uses the original anchor point).
>> This
>> >>>>>> probably will only work when molecules are both close in sequence
>> and
>> >>>>>> geometrically close.
>> >>>>>>
>> >>>>>> Try it and let me know if it works.
>> >>>>>>
>> >>>>>> -Dan
>> >>>>>>
>> >>>>>> On Tue, Jul 11, 2017 at 4:35 PM, Guqin Shi <shi.293.osu.edu> wrote:
>> >>>>>>> Oh my god...it just made my day...
>> >>>>>>> I've been desperately looking for solutions today... for example,
>> >> I am
>> >>>>>>> currently using the topotools plugged in VMD to write coordinates
>> >> of
>> >>>>>>> replicates from adjacent cells and trying to pick out the
>> >> coordinates
>> >>>> of
>> >>>>>> an
>> >>>>>>> intact complex...meantime I am worrying about the precision, the
>> >>>>>> potential
>> >>>>>>> artifacts, and speeds in processing massive of frames...
>> >>>>>>>
>> >>>>>>> -Guqin
>> >>>>>>>
>> >>>>>>> On Tue, Jul 11, 2017 at 3:52 PM, Daniel Roe <
>> >> daniel.r.roe.gmail.com>
>> >>>>>> wrote:
>> >>>>>>>> I think I have a fix (really a new autoimage option) that seems to
>> >>>>>>>> work. I'm testing now and will let you know when it's live.
>> >>>>>>>>
>> >>>>>>>> -Dan
>> >>>>>>>>
>> >>>>>>>> On Tue, Jul 11, 2017 at 11:46 AM, Guqin Shi <shi.293.osu.edu>
>> >> wrote:
>> >>>>>>>>> Hi Dan,
>> >>>>>>>>>
>> >>>>>>>>> this is really unfortunate but the unwrap doesn't work either...
>> >>>> The
>> >>>>>>>>> resulting coordinates are similar to autoimage/center-image that
>> >>>> one
>> >>>>>> of
>> >>>>>>>> the
>> >>>>>>>>> molecules is still left outside...
>> >>>>>>>>> In the Amber manual, there is a notation that "this command
>> >> fails
>> >>>> when
>> >>>>>>>> the
>> >>>>>>>>> masked molecules travel more than half of the box size within a
>> >>>> single
>> >>>>>>>>> frame." Is this the reason that unwrap couldn't work either...?
>> >>>>>>>>>
>> >>>>>>>>> I uploaded the raw coordinates of pr90 and the original input
>> >>>>>> coordinates
>> >>>>>>>>> pdb file into the folder. I also uploaded the an
>> >>>> test_unwrap_copy.in
>> >>>>>>>> file
>> >>>>>>>>> which contains the commands I used for reference-unwrap... I
>> >>>> comment
>> >>>>>> out
>> >>>>>>>>> center and image commands as since the unwrap failed, center and
>> >>>> image
>> >>>>>>>>> won't help much..
>> >>>>>>>>>
>> >>>>>>>>> If you have time, would you mind having a look at
>> >> them...Thanks...
>> >>>>>>>>> Best,
>> >>>>>>>>> Guqin
>> >>>>>>>>>
>> >>>>>>>>> On Tue, Jul 11, 2017 at 9:00 AM, Daniel Roe <
>> >>>> daniel.r.roe.gmail.com>
>> >>>>>>>> wrote:
>> >>>>>>>>>> Wow - this is certainly a challenging system to image! No one
>> >>>>>> molecule
>> >>>>>>>>>> can be considered "center" - in fact, there isn't even a region
>> >>>> of a
>> >>>>>>>>>> molecule that can be considered to be the center since when the
>> >>>>>>>>>> hexamer is formed there is a large empty space in the center
>> >> (from
>> >>>>>>>>>> looking at the system this appears to be the way it should be
>> >>>>>>>>>> assembled).
>> >>>>>>>>>>
>> >>>>>>>>>> I'll have to think about the best way to address this. In the
>> >>>>>>>>>> meantime, here is a potential workaround. You could unwrap the
>> >>>> entire
>> >>>>>>>>>> trajectory using the original input coordinates as a reference
>> >>>>>>>>>> (assuming the hexamer is "properly" formed there). You would
>> >> have
>> >>>> to
>> >>>>>>>>>> make certain you unwrap the trajectory in the right order,
>> >> i.e. in
>> >>>>>> the
>> >>>>>>>>>> same order it was simulated. You can then center on the hexamer
>> >>>> but
>> >>>>>>>>>> *only* image the water (and ions). So e.g.
>> >>>>>>>>>>
>> >>>>>>>>>> parm 1P9M_Hexamer.prmtop
>> >>>>>>>>>> reference pr90.rst7
>> >>>>>>>>>> trajin run0.nc
>> >>>>>>>>>> trajin run1.nc
>> >>>>>>>>>> ...
>> >>>>>>>>>> unwrap reference
>> >>>>>>>>>> center :1-1330
>> >>>>>>>>>> image :WAT,Na+
>> >>>>>>>>>>
>> >>>>>>>>>> The idea is to keep the hexamer together by effectively never
>> >>>> imaging
>> >>>>>>>>>> it, then reimaging all the mobile stuff so it looks nice. I
>> >> think
>> >>>>>>>>>> (hope) this will work.
>> >>>>>>>>>>
>> >>>>>>>>>> Thanks for the files!
>> >>>>>>>>>>
>> >>>>>>>>>> -Dan
>> >>>>>>>>>>
>> >>>>>>>>>> On Mon, Jul 10, 2017 at 1:05 PM, Guqin Shi <shi.293.osu.edu>
>> >>>> wrote:
>> >>>>>>>>>>> Hi Dan,
>> >>>>>>>>>>>
>> >>>>>>>>>>> In addition to visualize trajectories pleasantly...my main
>> >>>> purpose
>> >>>>>> is
>> >>>>>>>> to
>> >>>>>>>>>>> get correct coordinates so that the following MMPBSA
>> >> calculation
>> >>>>>>>> could be
>> >>>>>>>>>>> carried out... (or maybe MMPBSA doesn't care about that at
>> >>>>>> all...???
>> >>>>>>>>>> then I
>> >>>>>>>>>>> was wasting lots of my time...)
>> >>>>>>>>>>>
>> >>>>>>>>>>> I attached a prmtop with solvents stripped and a 1 ns of
>> >>>>>>>>>> nowat_coordinates
>> >>>>>>>>>>> (for the sake of file size) which I keep having problem
>> >> imaging
>> >>>>>> it...
>> >>>>>>>> (
>> >>>>>>>>>>> https://drive.google.com/open?id=
>> >> 0B7kncIsWo85uSWJmbFBtczNtdFE)
>> >>>>>> Please
>> >>>>>>>>>> let
>> >>>>>>>>>>> me know if you feel solvated coordinates are needed...
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>> Thanks a lot!!!
>> >>>>>>>>>>> -Guqin
>> >>>>>>>>>>>
>> >>>>>>>>>>> On Mon, Jul 10, 2017 at 12:29 PM, Daniel Roe <
>> >>>>>> daniel.r.roe.gmail.com>
>> >>>>>>>>>> wrote:
>> >>>>>>>>>>>> Hi,
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> (Could you send me some coordinates to go along with that
>> >>>> topology
>> >>>>>>>>>> file?)
>> >>>>>>>>>>>> On Mon, Jul 10, 2017 at 12:15 PM, Guqin Shi <
>> >> shi.293.osu.edu>
>> >>>>>> wrote:
>> >>>>>>>>>>>>> at the bottom edge of box......According to the original
>> >>>> prmtop
>> >>>>>>>> files,
>> >>>>>>>>>>>> the
>> >>>>>>>>>>>>> complex sits at the center of water box, but also
>> >> meantime,
>> >>>> it
>> >>>>>> sits
>> >>>>>>>>>> along
>> >>>>>>>>>>>>> the diagonal line...It seems center-image puts molecule
>> >> along
>> >>>>>> any
>> >>>>>>>> of
>> >>>>>>>>>> the
>> >>>>>>>>>>>>> side line and that's why it just couldn't fit all back...?
>> >>>> But I
>> >>>>>>>> am so
>> >>>>>>>>>>>>> confused now as why early trajectories could be imaged
>> >>>> without
>> >>>>>> any
>> >>>>>>>>>>>>> problem...
>> >>>>>>>>>>>> Re-imaging is more of an art than a science, mostly because
>> >>>>>> imaging
>> >>>>>>>> is
>> >>>>>>>>>>>> something that we do to make things "look nice". The
>> >> molecules
>> >>>>>> being
>> >>>>>>>>>>>> simulated don't care where they are absolutely, they only
>> >> care
>> >>>>>> where
>> >>>>>>>>>>>> they are with respect to other molecules. When you center on
>> >>>> one
>> >>>>>>>>>>>> molecule, you shift the coordinates of the entire system,
>> >> some
>> >>>> of
>> >>>>>>>>>>>> which move past the boundaries of your unit cell. Those
>> >> atoms
>> >>>> are
>> >>>>>>>> then
>> >>>>>>>>>>>> "wrapped" or re-imaged back inside the unit cell, which is
>> >> what
>> >>>>>> can
>> >>>>>>>>>>>> result in molecules appearing "separated". The 'autoimage'
>> >>>> command
>> >>>>>>>>>>>> tries to image in a way that keeps these molecules together
>> >> by
>> >>>>>>>>>>>> defining an anchor molecule/region (which is at the center),
>> >>>> and
>> >>>>>>>>>>>> molecules that are "fixed" to that anchor - it then tries to
>> >>>>>> minimize
>> >>>>>>>>>>>> the distance between the anchor and fixed molecules. Where
>> >> this
>> >>>>>> fails
>> >>>>>>>>>>>> is when a "wrapped" version of the system has shorter
>> >> distances
>> >>>>>> than
>> >>>>>>>>>>>> the "unwrapped version", which is typically because the
>> >>>>>> definition of
>> >>>>>>>>>>>> the anchor (center) is off. This is why the definition of
>> >> the
>> >>>>>>>> "anchor"
>> >>>>>>>>>>>> region is so crucial.
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> Send me those coordinates and I'll see what can be done.
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> -Dan
>> >>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Thanks,
>> >>>>>>>>>>>>> Guqin
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> On Mon, Jul 10, 2017 at 11:43 AM, Guqin Shi <
>> >>>> gshi.cop.ufl.edu>
>> >>>>>>>> wrote:
>> >>>>>>>>>>>>>> On Mon, Jul 10, 2017 at 8:32 AM, Daniel Roe <
>> >>>>>>>> daniel.r.roe.gmail.com>
>> >>>>>>>>>>>>>> wrote:
>> >>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>> Hi,
>> >>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>> The key for 'autoimage' is that you need to specify a
>> >>>> region
>> >>>>>>>>>>>>>>> (molecule, residue, atom, etc) that visually you want to
>> >>>> be at
>> >>>>>>>> the
>> >>>>>>>>>>>>>>> center of your unit cell; in cpptraj this is called the
>> >>>>>>>> 'anchor'. By
>> >>>>>>>>>>>>>>> default 'autoimage' tries to use the first molecule to
>> >> do
>> >>>>>> this.
>> >>>>>>>>>>>>>>> However in certain systems another choice is better. For
>> >>>>>>>> example, if
>> >>>>>>>>>>>>>>> you have a dimer then you would want to choose 1 or more
>> >>>>>> residues
>> >>>>>>>>>> that
>> >>>>>>>>>>>>>>> are near the center of the interface between the two
>> >>>> monomers
>> >>>>>> as
>> >>>>>>>>>> your
>> >>>>>>>>>>>>>>> anchor. Without seeing your system I can't make specific
>> >>>>>>>>>>>>>>> recommendations, but you could try experimenting with
>> >>>>>> different
>> >>>>>>>>>> anchor
>> >>>>>>>>>>>>>>> points. If you'd like, send me a PDB file or
>> >>>> topology/restart
>> >>>>>>>> files
>> >>>>>>>>>> of
>> >>>>>>>>>>>>>>> your system off-list and I can try to recommend an
>> >> anchor.
>> >>>>>>>>>>>>>>> -Dan
>> >>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>> Hi Bill,
>> >>>>>>>>>>>>>>
>> >>>>>>>>>>>>>> Thanks for pointing out the key point of "autoimage". I
>> >>>> tried
>> >>>>>> to
>> >>>>>>>> play
>> >>>>>>>>>>>> with
>> >>>>>>>>>>>>>> autoimage-anchor a little bit by myself. I noticed that
>> >> the
>> >>>>>> mask
>> >>>>>>>> for
>> >>>>>>>>>>>>>> autoimage are molecule-wise, instead of residue-wise...
>> >>>>>> Therefore
>> >>>>>>>>>> when I
>> >>>>>>>>>>>>>> specify some center residues, cpptraj reports back with
>> >>>> error
>> >>>>>>>> (Error:
>> >>>>>>>>>>>>>> Anchor mask [:153-155] corresponds to 0 mols, should
>> >> only be
>> >>>>>> 1.)
>> >>>>>>>> and
>> >>>>>>>>>>>> then
>> >>>>>>>>>>>>>> it goes with default again... Maybe my syntax is somehow
>> >> not
>> >>>>>>>> correct?
>> >>>>>>>>>>>>>> Also, my system is a little bit special. It is a "dimer"
>> >> and
>> >>>>>> each
>> >>>>>>>>>>>> monomer
>> >>>>>>>>>>>>>> contains three molecules. There is a hollow in between
>> >> the
>> >>>> two
>> >>>>>>>>>> dimers...
>> >>>>>>>>>>>>>> Currently in my own practice, I picked three residues on
>> >>>> each
>> >>>>>> of
>> >>>>>>>> the
>> >>>>>>>>>>>> dimer
>> >>>>>>>>>>>>>> which I think, are the closest to the center of cell
>> >>>> (143-155 &
>> >>>>>>>>>>>> 818-820).
>> >>>>>>>>>>>>>> Also, since these residues are symmetric, I am not sure
>> >> how
>> >>>> the
>> >>>>>>>>>> program
>> >>>>>>>>>>>>>> would place them in terms of direction...or maybe in this
>> >>>> case,
>> >>>>>>>>>>>> asymmetric
>> >>>>>>>>>>>>>> residues might be better...? I attached the prmtop file
>> >>>> (with
>> >>>>>>>>>>>> solvens/ions)
>> >>>>>>>>>>>>>> here on my google drive:
>> >>>>>>>>>>>>>> https://drive.google.com/open?id=
>> >>>> 0B7kncIsWo85ud1BweGJfd1h1ZXM
>> >>>>>>>>>> (Since it
>> >>>>>>>>>>>>>> is quite big so I don't think mailing list server would
>> >>>> allow
>> >>>>>> that
>> >>>>>>>>>>>> size..)
>> >>>>>>>>>>>>>> Could you also check my system to see if my choice on
>> >>>> residues
>> >>>>>> are
>> >>>>>>>>>> good
>> >>>>>>>>>>>> or
>> >>>>>>>>>>>>>> maybe another set of residues are better..?
>> >>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>
>> >>>>>>>>>>>>>> Thanks a lot for your help!
>> >>>>>>>>>>>>>> -Guqin
>> >>>>>>>>>>>>>>
>> >>>>>>>>>>>>>> --
>> >>>>>>>>>>>>>> Guqin SHI
>> >>>>>>>>>>>>>> 1345 Center Drive
>> >>>>>>>>>>>>>> College of Pharmacy
>> >>>>>>>>>>>>>> PO Box 100485
>> >>>>>>>>>>>>>> University of Florida
>> >>>>>>>>>>>>>> Gainesville, FL 32610
>> >>>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> --
>> >>>>>>>>>>>>> Guqin SHI
>> >>>>>>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy
>> >>>>>>>>>>>>> College of Pharmacy
>> >>>>>>>>>>>>> The Ohio State University
>> >>>>>>>>>>>>> Columbus, OH, 43210
>> >>>>>>>>>>>>> _______________________________________________
>> >>>>>>>>>>>>> AMBER mailing list
>> >>>>>>>>>>>>> AMBER.ambermd.org
>> >>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>>>>>>>>>>
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> --
>> >>>>>>>>>>>> -------------------------
>> >>>>>>>>>>>> Daniel R. Roe
>> >>>>>>>>>>>> Laboratory of Computational Biology
>> >>>>>>>>>>>> National Institutes of Health, NHLBI
>> >>>>>>>>>>>> 5635 Fishers Ln, Rm T900
>> >>>>>>>>>>>> Rockville MD, 20852
>> >>>>>>>>>>>> https://www.lobos.nih.gov/lcb
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> _______________________________________________
>> >>>>>>>>>>>> AMBER mailing list
>> >>>>>>>>>>>> AMBER.ambermd.org
>> >>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>> --
>> >>>>>>>>>>> Guqin SHI
>> >>>>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy
>> >>>>>>>>>>> College of Pharmacy
>> >>>>>>>>>>> The Ohio State University
>> >>>>>>>>>>> Columbus, OH, 43210
>> >>>>>>>>>>> _______________________________________________
>> >>>>>>>>>>> AMBER mailing list
>> >>>>>>>>>>> AMBER.ambermd.org
>> >>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> --
>> >>>>>>>>>> -------------------------
>> >>>>>>>>>> Daniel R. Roe
>> >>>>>>>>>> Laboratory of Computational Biology
>> >>>>>>>>>> National Institutes of Health, NHLBI
>> >>>>>>>>>> 5635 Fishers Ln, Rm T900
>> >>>>>>>>>> Rockville MD, 20852
>> >>>>>>>>>> https://www.lobos.nih.gov/lcb
>> >>>>>>>>>>
>> >>>>>>>>>> _______________________________________________
>> >>>>>>>>>> AMBER mailing list
>> >>>>>>>>>> AMBER.ambermd.org
>> >>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> --
>> >>>>>>>>> Guqin SHI
>> >>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy
>> >>>>>>>>> College of Pharmacy
>> >>>>>>>>> The Ohio State University
>> >>>>>>>>> Columbus, OH, 43210
>> >>>>>>>>> _______________________________________________
>> >>>>>>>>> AMBER mailing list
>> >>>>>>>>> AMBER.ambermd.org
>> >>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>> --
>> >>>>>>>> -------------------------
>> >>>>>>>> Daniel R. Roe
>> >>>>>>>> Laboratory of Computational Biology
>> >>>>>>>> National Institutes of Health, NHLBI
>> >>>>>>>> 5635 Fishers Ln, Rm T900
>> >>>>>>>> Rockville MD, 20852
>> >>>>>>>> https://www.lobos.nih.gov/lcb
>> >>>>>>>>
>> >>>>>>>> _______________________________________________
>> >>>>>>>> AMBER mailing list
>> >>>>>>>> AMBER.ambermd.org
>> >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> --
>> >>>>>>> Guqin SHI
>> >>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy
>> >>>>>>> College of Pharmacy
>> >>>>>>> The Ohio State University
>> >>>>>>> Columbus, OH, 43210
>> >>>>>>> _______________________________________________
>> >>>>>>> AMBER mailing list
>> >>>>>>> AMBER.ambermd.org
>> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>>>>
>> >>>>>>
>> >>>>>> --
>> >>>>>> -------------------------
>> >>>>>> Daniel R. Roe
>> >>>>>> Laboratory of Computational Biology
>> >>>>>> National Institutes of Health, NHLBI
>> >>>>>> 5635 Fishers Ln, Rm T900
>> >>>>>> Rockville MD, 20852
>> >>>>>> https://www.lobos.nih.gov/lcb
>> >>>>>>
>> >>>>>> _______________________________________________
>> >>>>>> AMBER mailing list
>> >>>>>> AMBER.ambermd.org
>> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>>>>
>> >>>>>
>> >>>>>
>> >>>>> --
>> >>>>> Guqin SHI
>> >>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy
>> >>>>> College of Pharmacy
>> >>>>> The Ohio State University
>> >>>>> Columbus, OH, 43210
>> >>>>> _______________________________________________
>> >>>>> AMBER mailing list
>> >>>>> AMBER.ambermd.org
>> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>>
>> >>>>
>> >>>> --
>> >>>> -------------------------
>> >>>> Daniel R. Roe
>> >>>> Laboratory of Computational Biology
>> >>>> National Institutes of Health, NHLBI
>> >>>> 5635 Fishers Ln, Rm T900
>> >>>> Rockville MD, 20852
>> >>>> https://www.lobos.nih.gov/lcb
>> >>>>
>> >>>> _______________________________________________
>> >>>> AMBER mailing list
>> >>>> AMBER.ambermd.org
>> >>>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>>
>> >>>
>> >>>
>> >>> --
>> >>> Guqin SHI
>> >>> PhD Candidate in Medicinal Chemistry and Pharmacognosy
>> >>> College of Pharmacy
>> >>> The Ohio State University
>> >>> Columbus, OH, 43210
>> >>>
>> >>> _______________________________________________
>> >>> AMBER mailing list
>> >>> AMBER.ambermd.org
>> >>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>
>> >>
>> >>
>> >> --
>> >> -------------------------
>> >> Daniel R. Roe
>> >> Laboratory of Computational Biology
>> >> National Institutes of Health, NHLBI
>> >> 5635 Fishers Ln, Rm T900
>> >> Rockville MD, 20852
>> >> https://www.lobos.nih.gov/lcb
>> >>
>> >> _______________________________________________
>> >> 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
>>
>
>
>
> --
> Guqin SHI
> PhD Candidate in Medicinal Chemistry and Pharmacognosy
> College of Pharmacy
> The Ohio State University
> Columbus, OH, 43210
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Jul 12 2017 - 15:30:04 PDT
