.Bill: Speed is not an issue in pytraj (users can use numpy or cython
for C/Fortran speed).
However, it will be hard for users to implement if they are not get
used to do programming. :D
Btw, we have Dan. And the enhancement in cpptraj automatically appear in pytraj.
cheers
Hai
On Wed, Jul 12, 2017 at 6:07 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> 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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> AMBER mailing list
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Received on Wed Jul 12 2017 - 15:30:03 PDT
