Dear Daniel,
The I would like to calculate the hydrogen bonding lifetimes in my bilayer
system.
For hbond calculation I executed this command:
*hbond MyHB :1-128 dist 3.5 angle 120 \ avgout avghb.dat nointramol series
\ solventacceptor :WAT.O solventdonor :WAT \ solvout solvent_avg.dat
bridgeout bridge.datrunwritedata nhb.dat MyHB[UU] MyHB[UV]
MyHB[Bridge]writedata solutehb.dat MyHB[solutehb]writedata solventhb.dat
MyHB[solventhb]lifetime MyHB[solutehb] out
solute.lifetime.datlifetime MyHB[solventhb] out
solvent.lifetime.datrunanalysis*
>From above command (the two lines):
*lifetime MyHB[solutehb] out solute.lifetime.dat*
*lifetime MyHB[solventhb] out solvent.lifetime.dat*
generate two files with lifetime information. The
*solute.lifetime.dat* contain
info like:
#Set Nlifetimes MaxLT AvgLT TotFrames SetName
0 22 1 1.0000 22
BMR_3.O16-BMR_1.O22-H22
1 296 346 15.6959 4646
BMR_42.O22-BMR_1.O22-H22
2 992 12 1.4688 1457
BMR_42.O14-BMR_1.O22-H22
3 1 1 1.0000 1
BMR_42.O13-BMR_1.O22-H22
4 189 12 1.1429 216
BMR_57.O25-BMR_1.O22-H22
5 462 410 12.3074 5686
BMR_57.O16-BMR_1.O22-H22
I would like to know how I can go from here to calculate the hb-lifetime
between solute and solute?
I think simple example would help me much in this case.
You help is much appreciated.
Thank you.
Vijay
On Thu, Feb 12, 2015 at 11:40 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Thu, Feb 12, 2015 at 8:28 AM, Vijay Achari <glycoamber.gmail.com>
> wrote:
> > With your latest code, the calculation run fine.
>
> OK, this seems like it is a buffer overflow problem caused by long
> bridge ID strings. I'll have to work on a patch for that.
>
> > The *nhb.dat* file contains information as below
> >
> > *#Frame MyHB[UU] MyHB[UV] MyHB[Bridge]*
> > 1 315 979 190
> >
> > Well, if I not mistaken this is the file called as *<dsetarg0>* (data
> set)
> > for calculating the *lifetime*?
>
> No, this is just the number of solute-solute hydrogen bonds,
> solute-solvent hydrogen bonds, and solute-solvent bridges
> respectively. The MyHB[solutehb] etc data sets contain the hydrogen
> bond time series data that is used for the lifetime calculation (1 if
> hydrogen bond is present, 0 if not).
>
> -Dan
>
> >
> > Regards
> > Vijay
> >
> >
> >
> > On Thu, Feb 12, 2015 at 11:06 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> OK, try it again but remove 'out nhb.dat' from your hbond command.
> >> Then add one more command after 'run', e.g.:
> >>
> >> hbond MyHB :1-128 dist 3.5 angle 120 \
> >> avgout avghb.dat nointramol series \
> >> solventacceptor :WAT.O solventdonor :WAT \
> >> solvout solvent_avg.dat bridgeout bridge.dat
> >> run
> >> writedata nhb.dat MyHB[UU] MyHB[UV] MyHB[Bridge]
> >>
> >> See if that works,
> >>
> >> -Dan
> >>
> >> On Thu, Feb 12, 2015 at 7:51 AM, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >> > This is strange, and may indicate a bug. I will try to reproduce the
> >> > error on my end and get back to you.
> >> >
> >> > -Dan
> >> >
> >> > On Thu, Feb 12, 2015 at 2:19 AM, Vijay Achari <glycoamber.gmail.com>
> >> wrote:
> >> >> Dear Dan,
> >> >>
> >> >> I ran this whole calculation in another machine which have 96GB of
> RAM
> >> and
> >> >> 24 core processors running in CENTOS6.
> >> >>
> >> >> I created a input file which contains:
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> *trajin
> >> >>
> >>
> /home/users/vijay/slot3/paper3-lyo-system-TRAJ-Only/onlyTraj-bcmLyo25perR/reImaged-bcmLyo25perR.nc
> >> >> 15001 15010hbond MyHB :1-128 out nhb.dat dist 3.5 angle 120 avgout
> >> >> avghb.dat \ nointramol series solventacceptor :WAT.O solventdonor
> >> :WAT
> >> >> \ solvout solvent_avg.dat bridgeout bridge.datrunwritedata
> >> solutehb.dat
> >> >> MyHB[solutehb]writedata solventhb.dat MyHB[solventhb]lifetime
> >> >> MyHB[solutehb] out solute.lifetime.datlifetime MyHB[solventhb] out
> >> >> solvent.lifetime.datrunanalysis*
> >> >> and I executed this file using cpptraj command:
> >> >>
> >> >>
> >> >> *cpptraj topology -i hb-cpptraj2.in <http://hb-cpptraj2.in>*
> >> >> If you notice, I only choose 10 frames. and the calculation run fine.
> >> But
> >> >> at the end it states as below:
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> * . . . . MyHB[solventhb]:12640 "BMR_121.O15-V"
> >> >> (integer), size is 10 MyHB[solventhb]:8317 "BMR_80.O14-V"
> (integer),
> >> >> size is 10 MyHB[solventhb]:8647 "BMR_83.O16-V" (integer), size
> is 10
> >> >> MyHB[solventhb]:9574 "BMR_92.O25-V" (integer), size is 10
> >> >> MyHB[solventhb]:964 "BMR_10.O25-V" (integer), size is 10
> >> >> MyHB[solventhb]:3465 "BMR_34.O22-V" (integer), size is 10
> >> >> MyHB[solventhb]:4531 "BMR_44.O26-V" (integer), size is 10
> >> >> MyHB[solventhb]:3694 "BMR_36.O25-V" (integer), size is 10
> >> >> MyHB[solventhb]:4324 "BMR_42.O25-V" (integer), size is 10DATAFILES:
> >> >> nhb.dat (Standard Data File): MyHB[UU] MyHB[UV] MyHB[Bridge]
> >> >> MyHB[ID]Segmentation fault (core dumped)*
> >> >> I get three files avghb.dat, bridge.dat, *nhb.dat* and
> solvent_avg.dat.
> >> But
> >> >> the nhb.dat file is empty. There is no data at all.
> >> >>
> >> >> Other files contains data in their respective formats.
> >> >>
> >> >> Why this happens and how to overcome?
> >> >> Your help is much appreciated.
> >> >>
> >> >> Thank you.
> >> >>
> >> >> Vijay
> >> >>
> >> >>
> >> >> On Thu, Feb 12, 2015 at 1:46 PM, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >> >>
> >> >>> Hi,
> >> >>>
> >> >>> On Wed, Feb 11, 2015 at 6:32 PM, Vijay Achari <glycoamber.gmail.com
> >
> >> >>> wrote:
> >> >>> > Is this showing some error?
> >> >>> >
> >> >>> >
> >> >>> >
> >> >>> > DATAFILES:
> >> >>> > nhb.dat (Standard Data File): MyHB[UU] MyHB[UV] MyHB[Bridge]
> >> MyHB[ID]
> >> >>> > *** buffer overflow detected ***: cpptraj terminated
> >> >>>
> >> >>> Interesting - this indicates a memory issue. What version of cpptraj
> >> >>> are you using (cpptraj --version)? What happens if you write out in
> >> >>> grace format instead (change nhb.dat to nhb.avg)? The hbond time
> >> >>> series command can be very memory hungry since you essentially need
> an
> >> >>> array of size N (where N is the number of frames) for each hydrogen
> >> >>> bond detected. What happens if you run without the 'series' keyword?
> >> >>>
> >> >>> -Dan
> >> >>>
> >> >>> > ======= Backtrace: =========
> >> >>> > /lib/x86_64-linux-gnu/libc.so.6(+0x73f1f)[0x7f917d6fdf1f]
> >> >>> >
> /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f917d79582c]
> >> >>> > /lib/x86_64-linux-gnu/libc.so.6(+0x10a6f0)[0x7f917d7946f0]
> >> >>> > /lib/x86_64-linux-gnu/libc.so.6(+0x109bf9)[0x7f917d793bf9]
> >> >>> >
> >> /lib/x86_64-linux-gnu/libc.so.6(_IO_default_xsputn+0xbc)[0x7f917d70629c]
> >> >>> > /lib/x86_64-linux-gnu/libc.so.6(_IO_padn+0x6e)[0x7f917d6fa22e]
> >> >>> >
> /lib/x86_64-linux-gnu/libc.so.6(_IO_vfprintf+0x2576)[0x7f917d6d6266]
> >> >>> >
> /lib/x86_64-linux-gnu/libc.so.6(__vsprintf_chk+0x84)[0x7f917d793c84]
> >> >>> > cpptraj[0x520100]
> >> >>> > cpptraj[0x5335fb]
> >> >>> > cpptraj[0x533ae2]
> >> >>> > cpptraj[0x53655a]
> >> >>> > cpptraj[0x526d93]
> >> >>> > cpptraj[0x527aaf]
> >> >>> > cpptraj[0x524a70]
> >> >>> > cpptraj[0x516442]
> >> >>> > cpptraj[0x51677b]
> >> >>> > cpptraj[0x51e8f9]
> >> >>> > cpptraj[0x51f3b5]
> >> >>> > cpptraj[0x40a201]
> >> >>> >
> >> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f917d6abec5]
> >> >>> > cpptraj[0x40a26b]
> >> >>> > ======= Memory map: ========
> >> >>> > 00400000-0071c000 r-xp 00000000 08:06 420960
> >> >>> > /usr/local/apps/amber14/bin/cpptraj
> >> >>> > 0091c000-00969000 r--p 0031c000 08:06 420960
> >> >>> > /usr/local/apps/amber14/bin/cpptraj
> >> >>> > 00969000-00971000 rw-p 00369000 08:06 420960
> >> >>> > /usr/local/apps/amber14/bin/cpptraj
> >> >>> > 00971000-0098a000 rw-p 00000000 00:00 0
> >> >>> > 02924000-107b1000 rw-p 00000000 00:00 0
> >> >>> > [heap]
> >> >>> > 7f917cb4c000-7f917d00d000 rw-p 00000000 00:00 0
> >> >>> > 7f917d44e000-7f917d489000 r-xp 00000000 08:06 272697
> >> >>> > /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> >> >>> > 7f917d489000-7f917d688000 ---p 0003b000 08:06 272697
> >> >>> > /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> >> >>> > 7f917d688000-7f917d689000 r--p 0003a000 08:06 272697
> >> >>> > /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> >> >>> > 7f917d689000-7f917d68a000 rw-p 0003b000 08:06 272697
> >> >>> > /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> >> >>> > 7f917d68a000-7f917d845000 r-xp 00000000 08:06 683092
> >> >>> > /lib/x86_64-linux-gnu/libc-2.19.so
> >> >>> > 7f917d845000-7f917da45000 ---p 001bb000 08:06 683092
> >> >>> > /lib/x86_64-linux-gnu/libc-2.19.so
> >> >>> > 7f917da45000-7f917da49000 r--p 001bb000 08:06 683092
> >> >>> > /lib/x86_64-linux-gnu/libc-2.19.so
> >> >>> > 7f917da49000-7f917da4b000 rw-p 001bf000 08:06 683092
> >> >>> > /lib/x86_64-linux-gnu/libc-2.19.so
> >> >>> > 7f917da4b000-7f917da50000 rw-p 00000000 00:00 0
> >> >>> > 7f917da50000-7f917da66000 r-xp 00000000 08:06 659472
> >> >>> > /lib/x86_64-linux-gnu/libgcc_s.so.1
> >> >>> > 7f917da66000-7f917dc65000 ---p 00016000 08:06 659472
> >> >>> > /lib/x86_64-linux-gnu/libgcc_s.so.1
> >> >>> > 7f917dc65000-7f917dc66000 rw-p 00015000 08:06 659472
> >> >>> > /lib/x86_64-linux-gnu/libgcc_s.so.1
> >> >>> > 7f917dc66000-7f917dd6b000 r-xp 00000000 08:06 683111
> >> >>> > /lib/x86_64-linux-gnu/libm-2.19.so
> >> >>> > 7f917dd6b000-7f917df6a000 ---p 00105000 08:06 683111
> >> >>> > /lib/x86_64-linux-gnu/libm-2.19.so
> >> >>> > 7f917df6a000-7f917df6b000 r--p 00104000 08:06 683111
> >> >>> > /lib/x86_64-linux-gnu/libm-2.19.so
> >> >>> > 7f917df6b000-7f917df6c000 rw-p 00105000 08:06 683111
> >> >>> > /lib/x86_64-linux-gnu/libm-2.19.so./hb-Analysis.cpptraj: line 39:
> >> 2888
> >> >>> > Aborted (core dumped) cpptraj $top <<EOF
> >> >>> >
> >> >>> >
> >> >>> > trajin $trajpath/reImaged-$system.nc 15001 20000
> >> >>> >
> >> >>> >
> >> >>> > # COMMAND
> >> >>> >
> >> >>> > hbond MyHB :1-128 out nhb.dat dist 3.5 angle 120 avgout avghb.dat
> >> >>> > nointramol series solventacceptor :WAT.O solventdonor :WAT
> >> solvout
> >> >>> > solvent_avg.dat bridgeout bridge.dat
> >> >>> > run
> >> >>> > writedata solutehb.dat MyHB[solutehb]
> >> >>> > writedata solventhb.dat MyHB[solventhb]
> >> >>> > lifetime MyHB[solutehb] out solute.lifetime.dat
> >> >>> > lifetime MyHB[solventhb] out solvent.lifetime.dat
> >> >>> > runanalysis
> >> >>> >
> >> >>> >
> >> >>> > EOF
> >> >>> >
> >> >>> >
> >> >>> >
> >> >>> >
> >> >>> > Thank you
> >> >>> > Vijay
> >> >>> >
> >> >>> > On Thu, Feb 12, 2015 at 2:21 AM, Daniel Roe <
> daniel.r.roe.gmail.com>
> >> >>> wrote:
> >> >>> >
> >> >>> >> Hi,
> >> >>> >>
> >> >>> >> On Wed, Feb 11, 2015 at 10:35 AM, Vijay Achari <
> >> glycoamber.gmail.com>
> >> >>> >> wrote:
> >> >>> >> > So far I tried to execute a command as shown below:
> >> >>> >> >
> >> >>> >> > *hbond :1-128 out nhb.dat dist 3.5 angle 120 avgout avghb.dat
> >> >>> nointramol
> >> >>> >> > series*
> >> >>> >> >
> >> >>> >> > But I dont know what are the additional options I need to add
> in
> >> >>> order to
> >> >>> >> > calculate the solute-solvent (lipid-water) hydrogen bonding.
> And
> >> >>> continue
> >> >>> >> > with lifetime analysis, although you have mentioned about
> lifetime
> >> >>> >> > calculation in your earlier email.
> >> >>> >>
> >> >>> >> You will need to use the 'solventdonor' and 'solventacceptor'
> >> >>> >> keywords. I also recommend giving your hydrogen bond data set a
> name
> >> >>> >> to make it easier to refer to when writing out and analyzing your
> >> time
> >> >>> >> series data. So you may want to modify your input like so:
> >> >>> >>
> >> >>> >> hbond MyHB :1-128 out nhb.dat dist 3.5 angle 120 avgout
> avghb.dat \
> >> >>> >> nointramol series solventacceptor :WAT.O solventdonor :WAT \
> >> >>> >> solvout solvent_avg.dat bridgeout bridge.dat
> >> >>> >> run
> >> >>> >> writedata solutehb.dat MyHB[solutehb]
> >> >>> >> writedata solventhb.dat MyHB[solventhb]
> >> >>> >> lifetime MyHB[solutehb] out solute.lifetime.dat
> >> >>> >> lifetime MyHB[solventhb] out solvent.lifetime.dat
> >> >>> >> runanalysis
> >> >>> >>
> >> >>> >> The manual should definitely contain better examples, but it
> still
> >> has
> >> >>> >> some useful information. I highly recommend going over the manual
> >> >>> >> entries for the 'hbond' and 'lifetime' commands just to make sure
> >> you
> >> >>> >> understand what each keyword is doing. Hope that this helps, let
> me
> >> >>> >> know if you have any more questions.
> >> >>> >>
> >> >>> >> -Dan
> >> >>> >>
> >> >>> >> >
> >> >>> >> > Could you kindly help me here?
> >> >>> >> > Appreciate your help in advance.
> >> >>> >> >
> >> >>> >> > Thanks
> >> >>> >> > Vijay
> >> >>> >> >
> >> >>> >> >
> >> >>> >> > On Thu, Feb 12, 2015 at 12:44 AM, Daniel Roe <
> >> daniel.r.roe.gmail.com>
> >> >>> >> wrote:
> >> >>> >> >
> >> >>> >> >> Hi,
> >> >>> >> >>
> >> >>> >> >> On Wed, Feb 11, 2015 at 3:18 AM, Vijay Achari <
> >> glycoamber.gmail.com>
> >> >>> >> >> wrote:
> >> >>> >> >> > I don't understand the meaning of <*dsetarg0*> file. despite
> >> it is
> >> >>> >> saying
> >> >>> >> >> > about data file. But which data file and how to obtain this
> >> file?
> >> >>> >> >>
> >> >>> >> >> As stated in the manual, this argument pertains to data sets:
> >> >>> >> >>
> >> >>> >> >> <dsetarg0> [<dsetarg1> ...] Argument(s) specifying datasets
> to be
> >> >>> used.
> >> >>> >> >>
> >> >>> >> >> The data sets can be data that have been generated by cpptraj
> >> during
> >> >>> a
> >> >>> >> >> run, or previously read in with the 'readdata' command. For
> >> example,
> >> >>> >> >> say you have a data file named solventlifetime.dat which
> contains
> >> >>> >> >> hydrogen bond time series data (from 'hbond series') in
> columns,
> >> >>> e.g.:
> >> >>> >> >>
> >> >>> >> >> #Frame DC5_1.N3-V DC5_1.O2-V
> >> >>> >> >> 1 1.0000 1.0000
> >> >>> >> >> 2 0.0000 1.0000
> >> >>> >> >> ...
> >> >>> >> >>
> >> >>> >> >> You can read the data in and perform lifetime analysis (over
> >> windows
> >> >>> >> >> of size 5000) using the following input:
> >> >>> >> >>
> >> >>> >> >> readdata solventlifetime.dat
> >> >>> >> >> runanalysis lifetime out life.gnu solventlifetime.dat window
> 5000
> >> >>> >> >>
> >> >>> >> >> Note that since I didn't provide a data set name to the
> >> 'readdata'
> >> >>> >> >> command (via 'name <set name>'), the file name is chosen as
> >> default.
> >> >>> >> >> You can see what data sets are currently loaded with 'list
> >> dataset'.
> >> >>> >> >>
> >> >>> >> >> Note that the hydrogen bond time series data is not written
> out
> >> >>> >> >> automatically - you need to save it using a 'writedata'
> command
> >> after
> >> >>> >> >> 'hbond' is run, like so:
> >> >>> >> >>
> >> >>> >> >> parm ../DPDP.parm7
> >> >>> >> >> trajin ../DPDP.nc
> >> >>> >> >> hbond HB out hbond.dat .N,H,C,O series avgout hbavg.dat
> >> printatomnum
> >> >>> >> >> run
> >> >>> >> >> write solutehb.agr HB[solutehb]
> >> >>> >> >> runanalysis lifetime HB[solutehb] out lifehb.gnu window 10
> >> >>> >> >>
> >> >>> >> >> There are two things to note in the above input. The first is
> >> that I
> >> >>> >> >> am issuing a 'run' command before writing or performing
> analysis
> >> on
> >> >>> >> >> the hydrogen bond time series data. This is because unlike
> some
> >> other
> >> >>> >> >> commands (like e.g. 'distance'), cpptraj doesn't know if any
> >> data (in
> >> >>> >> >> this case hydrogen bonds) is actually present in the system
> >> until the
> >> >>> >> >> analysis is actually run. The second is that I'm using a data
> set
> >> >>> >> >> aspect (in this case [solutehb]) to select only solute-solute
> >> >>> hydrogen
> >> >>> >> >> bonds.
> >> >>> >> >>
> >> >>> >> >> This should be explained better in the manual, and there is a
> >> >>> tutorial
> >> >>> >> >> in the works, but for now I recommend you read section 28.3 of
> >> the
> >> >>> >> >> Amber 14 manual (Data Sets and Data Files), and maybe run
> >> through the
> >> >>> >> >> two existing cpptraj tutorials
> >> >>> >> >> (http://ambermd.org/tutorials/#analysis) to become more
> familiar
> >> >>> with
> >> >>> >> >> data sets etc in cpptraj.
> >> >>> >> >>
> >> >>> >> >> Hope this helps - let me know if you have any more questions,
> >> >>> >> >>
> >> >>> >> >> -Dan
> >> >>> >> >>
> >> >>> >> >>
> >> >>> >> >> >
> >> >>> >> >> > Anyway I tried something like below:
> >> >>> >> >> >
> >> >>> >> >> >
> >> >>> >> >> >
> >> >>> >> >> > cpptraj topology << EOF
> >> >>> >> >> >
> >> >>> >> >> > *lifetime out hb-LifeTime-bcmLyo25perR.out
> >> >>> >> >> > HB_inBothLayer_001_128-bcmLyo25perR.tbl cut 0.5 greater*
> >> >>> >> >> >
> >> >>> >> >> > EOF
> >> >>> >> >> >
> >> >>> >> >> >
> >> >>> >> >> >
> >> >>> >> >> >
> >> >>> >> >> > with *HB_inBothLayer_001_128-bcmLyo25perR.tbl * is the
> output
> >> file
> >> >>> of
> >> >>> >> >> > hydrogen bonding.
> >> >>> >> >> >
> >> >>> >> >> > But this fail to run.
> >> >>> >> >> > I wish to get some here.
> >> >>> >> >> >
> >> >>> >> >> > Regards
> >> >>> >> >> > Vijay
> >> >>> >> >> > _______________________________________________
> >> >>> >> >> > AMBER mailing list
> >> >>> >> >> > AMBER.ambermd.org
> >> >>> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >>> >> >>
> >> >>> >> >>
> >> >>> >> >>
> >> >>> >> >> --
> >> >>> >> >> -------------------------
> >> >>> >> >> Daniel R. Roe, PhD
> >> >>> >> >> Department of Medicinal Chemistry
> >> >>> >> >> University of Utah
> >> >>> >> >> 30 South 2000 East, Room 307
> >> >>> >> >> Salt Lake City, UT 84112-5820
> >> >>> >> >> http://home.chpc.utah.edu/~cheatham/
> >> >>> >> >> (801) 587-9652
> >> >>> >> >> (801) 585-6208 (Fax)
> >> >>> >> >>
> >> >>> >> >> _______________________________________________
> >> >>> >> >> 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
> >> >>> >>
> >> >>> >>
> >> >>> >>
> >> >>> >> --
> >> >>> >> -------------------------
> >> >>> >> Daniel R. Roe, PhD
> >> >>> >> Department of Medicinal Chemistry
> >> >>> >> University of Utah
> >> >>> >> 30 South 2000 East, Room 307
> >> >>> >> Salt Lake City, UT 84112-5820
> >> >>> >> http://home.chpc.utah.edu/~cheatham/
> >> >>> >> (801) 587-9652
> >> >>> >> (801) 585-6208 (Fax)
> >> >>> >>
> >> >>> >> _______________________________________________
> >> >>> >> 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
> >> >>>
> >> >>>
> >> >>>
> >> >>> --
> >> >>> -------------------------
> >> >>> Daniel R. Roe, PhD
> >> >>> Department of Medicinal Chemistry
> >> >>> University of Utah
> >> >>> 30 South 2000 East, Room 307
> >> >>> Salt Lake City, UT 84112-5820
> >> >>> http://home.chpc.utah.edu/~cheatham/
> >> >>> (801) 587-9652
> >> >>> (801) 585-6208 (Fax)
> >> >>>
> >> >>> _______________________________________________
> >> >>> 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
> >> >
> >> >
> >> >
> >> > --
> >> > -------------------------
> >> > Daniel R. Roe, PhD
> >> > Department of Medicinal Chemistry
> >> > University of Utah
> >> > 30 South 2000 East, Room 307
> >> > Salt Lake City, UT 84112-5820
> >> > http://home.chpc.utah.edu/~cheatham/
> >> > (801) 587-9652
> >> > (801) 585-6208 (Fax)
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 307
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
> >> 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
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Mar 10 2015 - 00:00:02 PDT
