Hi Guqin,
> 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.
I don't know about python speed for such tasks. Likely optimizations are
possible. E.g. that inner 'if' I mentioned shouldn't be necessary, and
maybe something could be done with centroids of molecules. And one would
only calc inter-molecular distances, not the intra's since they would be
constant.
It's just a suggestion on my part, since I'm not working in the field.
Regards,
Bill
On 7/12/17 2:54 PM, Guqin Shi 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.
>
> 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
>>
>
>
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Received on Wed Jul 12 2017 - 15:30:02 PDT
