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.
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
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Received on Wed Jul 12 2017 - 15:00:04 PDT
