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
>>
>
>
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Received on Wed Jul 12 2017 - 15:00:03 PDT
