Dear Sir,
Thank you very much for your reply.
I have installed Amber14+amberTool15, but PLUMED was not patched successfully. So I changed from tool14 to tool15.
If AmberTools 15 is bundled with PLUMED support, is this means that I only need to install Amber14+amberTool15 and PLUMED seperately, Amber can use PLUMED directly. Is there any additional settings in the process of using £¿
Thans and best regards!
Xiaofeng Ji
At 2016-03-18 03:00:01, amber-request.ambermd.org wrote:
>Send AMBER mailing list submissions to
> amber.ambermd.org
>
>To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.ambermd.org/mailman/listinfo/amber
>or, via email, send a message with subject or body 'help' to
> amber-request.ambermd.org
>
>You can reach the person managing the list at
> amber-owner.ambermd.org
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of AMBER digest..."
>
>
>AMBER Mailing List Digest
>
>Today's Topics:
>
> 1. Re: rmsd y axis value deviation. (Saman Yousuf ali)
> 2. Re: rmsd y axis value deviation. (Daniel Roe)
> 3. Re: rmsd y axis value deviation. (Saman Yousuf ali)
> 4. ???Re: shell script (yhzahsc)
> 5. GROMACS File Conversion Subtlety (Robert Molt)
> 6. Re: calculate free energy binding in presence of ions witn
> mmpbsa (Josh Berryman)
> 7. errors in plumed and amber14 patch (jixiaofeng)
> 8. Re: errors in plumed and amber14 patch
> (hannes.loeffler.stfc.ac.uk)
> 9. 2016 ISQBP Meeting: early registration / abstract submission
> deadline approaching (Vlad Cojocaru)
> 10. Re: errors in plumed and amber14 patch (Jason Swails)
> 11. Amber 14 - "Error: Unsupported CUDA version 7.5 detected"
> (Enrique Frio)
> 12. Re: Error with make test.parallel in AmberTools 15
> installation (anu chandra)
> 13. Re: GROMACS File Conversion Subtlety (Daniel Roe)
> 14. Re: Amber 14 - "Error: Unsupported CUDA version 7.5 detected"
> (Ross Walker)
> 15. Training and Innovation Course in Drug Design (Thomas Exner)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Wed, 16 Mar 2016 19:04:40 +0000 (UTC)
>From: Saman Yousuf ali <saman.yousufali64.yahoo.com>
>Subject: Re: [AMBER] rmsd y axis value deviation.
>To: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>, AMBER Mailing List
> <amber.ambermd.org>
>Message-ID:
> <1372907554.1006156.1458155080144.JavaMail.yahoo.mail.yahoo.com>
>Content-Type: text/plain; charset=UTF-8
>
>Dear Loeffler,Thank you so much for your guidance and kind cooperation. I have also run cpptraj rmsd command using multiple trajin, as you recommended me. I got same valueon x-axis, 60000 frames. Kindly tell me the rms command, which has an option "time" to scale the x-axis or tell me link of manual. Input file and command are pasted below,input:
>trajin itk1.mdcrd
>trajin itk12.mdcrd
>trajin itk13.mdcrd
>trajin itk14.mdcrd
>trajin itk15.mdcrd
>trajin itk16.mdcrd
>trajin itk17.mdcrd
>trajin itk18.mdcrd
>trajin itk19.mdcrd
>trajin itk20.mdcrd
>trajin itk21.mdcrd
>trajin itk22.mdcrd
>trajin itk23.mdcrd
>trajin itk24.mdcrd
>trajin itk25.mdcrd
>trajin itk26.mdcrd
>trajin itk27.mdcrd
>trajin itk28.mdcrd
>trajin itk29.mdcrd
>trajin itk30.mdcrd
>center :1-263
>image familiar
>strip :WAT
>strip :NA+
>rms first out rmsd-zinctes.dat .C,CA,N time 10.0
>command:cpptraj -p itk.prmtop -i rmsd.in
>
>output:BEGIN TRAJECTORY PROCESSING:
>.....................................................
>ACTION SETUP FOR PARM 'itk.prmtop' (5 actions):
>? 0: [center :1-263]
>??????? Mask [:1-263] corresponds to 4177 atoms.
>? 1: [image familiar]
>??????? Number of molecules to be imaged is 9514 based on mask '*'
>? 2: [strip :WAT]
>??????? Stripping 28506 atoms.
>??????? Stripped parm: 'itk.prmtop', 4230 atoms, 274 res, box: Orthogonal, 12 mo
>l
>? 3: [strip :NA+]
>??????? Stripping 0 atoms.
>Warning: No atoms to strip. Skipping 'strip' for topology 'itk.prmtop'
>Warning: Setup failed for [strip :NA+]: Skipping
>? 4: [rms first out rmsd-zinctes.dat @C,CA,N time 2.0]
>??????? Target mask: [.C,CA,N](791)
>??????? Reference mask: [.C,CA,N](791)
>Warning: Coordinates are being rotated and box coordinates are present.
>Warning: Unit cell vectors are NOT rotated; imaging will not be possible
>Warning:? after the RMS-fit is performed.
>----- itk1.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk2.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk3.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk4.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk5.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk6.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk7.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk8.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk9.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk10.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk11.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk12.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk13.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk14.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk15.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk16.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk17.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk18.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk19.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk20.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk21.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk22.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk23.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk24.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk25.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk26.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk27.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk28.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk29.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>----- itk30.mdcrd (1-1000, 1) -----
>?0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
>Read 30000 frames and processed 30000 frames.
>TIME: Trajectory processing: 723.6999 s
>TIME: Avg. throughput= 41.4536 frames / second.
>
>ACTION OUTPUT:
>
>DATASETS:
>? 1 data set:
>??????? RMSD_00000 "RMSD_00000" (double, rms), size is 30000
>
>DATAFILES:
>? rmsd-zinctes.dat (Standard Data File):? RMSD_00000
>---------- RUN END ---------------------------------------------------
>TIME: Total execution time: 724.7298 seconds.
>--------------------------------------------------------------------------------
>To cite CPPTRAJ use:
>Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
>? Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
>? Theory Comput., 2013, 9 (7), pp 3084-3095.
>Thank you.
>?Best Regards, Saman Yousuf Ali
>
>
> On Wednesday, March 16, 2016 4:58 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
>
>
> On Wed, 16 Mar 2016 11:47:52 +0000
>Saman Yousuf ali <saman.yousufali64.yahoo.com> wrote:
>
>> trajin md_simulation_combine.nc
>> rms first :1-532.CA,C,N out rmsd.dat
>> strip :WATER
>> strip :Na+
>
>You are reading a single trajectory file here.? How many frames does it
>contain, how have you created this file?? Check this first.
>
>As far as cpptraj is concerned there is no need to combine trajectories
>beforehand.? I would recommend to use multiple "trajin" commands to
>read in the original files.
>
>The rms command has an option "time" which you can use to scale the
>x-axis to your liking.? See the manual.? If you do not use "time" then
>the x-axis is simply the number of frames.? So why does the file
>md_simulation_combine.nc have so many?? You originally indicated there
>should be only half that number.
>
>The final "strip" commands don't seem to do anything useful here (unless
>your script is longer and you do something else with the stripped
>topology later).? I suspect that the ":WATER" mask should actually
>be ":WAT".
>
>
>
>
>------------------------------
>
>Message: 2
>Date: Wed, 16 Mar 2016 13:12:32 -0600
>From: Daniel Roe <daniel.r.roe.gmail.com>
>Subject: Re: [AMBER] rmsd y axis value deviation.
>To: Saman Yousuf ali <saman.yousufali64.yahoo.com>, AMBER Mailing List
> <amber.ambermd.org>
>Message-ID:
> <CAAC0qOb3PXAqGX_zcnQtuQ0sFO-8cNT-JXhV+ywr0VxF8fCTDQ.mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Hi,
>
>First, the input you posted doesn't correspond to the output. Here's
>the rms command from your input:
>
>On Wed, Mar 16, 2016 at 1:04 PM, Saman Yousuf ali
><saman.yousufali64.yahoo.com> wrote:
>> rms first out rmsd-zinctes.dat @C,CA,N time 10.0
>
>Here is the rms command in your output:
>
>> 4: [rms first out rmsd-zinctes.dat @C,CA,N time 2.0]
>
>Here you are setting the 'time' argument to 2.0, so cpptraj multiplies
>each frame you have by '2'. Since you have 30000 frames, the final X
>value is 60000.
>
>-Dan
>
>> Target mask: [.C,CA,N](791)
>> Reference mask: [.C,CA,N](791)
>> Warning: Coordinates are being rotated and box coordinates are present.
>> Warning: Unit cell vectors are NOT rotated; imaging will not be possible
>> Warning: after the RMS-fit is performed.
>> ----- itk1.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk2.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk3.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk4.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk5.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk6.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk7.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk8.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk9.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk10.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk11.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk12.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk13.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk14.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk15.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk16.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk17.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk18.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk19.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk20.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk21.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk22.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk23.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk24.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk25.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk26.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk27.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk28.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk29.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk30.mdcrd (1-1000, 1) -----
>> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> Read 30000 frames and processed 30000 frames.
>> TIME: Trajectory processing: 723.6999 s
>> TIME: Avg. throughput= 41.4536 frames / second.
>>
>> ACTION OUTPUT:
>>
>> DATASETS:
>> 1 data set:
>> RMSD_00000 "RMSD_00000" (double, rms), size is 30000
>>
>> DATAFILES:
>> rmsd-zinctes.dat (Standard Data File): RMSD_00000
>> ---------- RUN END ---------------------------------------------------
>> TIME: Total execution time: 724.7298 seconds.
>> --------------------------------------------------------------------------------
>> To cite CPPTRAJ use:
>> Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
>> Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
>> Theory Comput., 2013, 9 (7), pp 3084-3095.
>> Thank you.
>> Best Regards, Saman Yousuf Ali
>>
>>
>> On Wednesday, March 16, 2016 4:58 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
>>
>>
>> On Wed, 16 Mar 2016 11:47:52 +0000
>> Saman Yousuf ali <saman.yousufali64.yahoo.com> wrote:
>>
>>> trajin md_simulation_combine.nc
>>> rms first :1-532.CA,C,N out rmsd.dat
>>> strip :WATER
>>> strip :Na+
>>
>> You are reading a single trajectory file here. How many frames does it
>> contain, how have you created this file? Check this first.
>>
>> As far as cpptraj is concerned there is no need to combine trajectories
>> beforehand. I would recommend to use multiple "trajin" commands to
>> read in the original files.
>>
>> The rms command has an option "time" which you can use to scale the
>> x-axis to your liking. See the manual. If you do not use "time" then
>> the x-axis is simply the number of frames. So why does the file
>> md_simulation_combine.nc have so many? You originally indicated there
>> should be only half that number.
>>
>> The final "strip" commands don't seem to do anything useful here (unless
>> your script is longer and you do something else with the stripped
>> topology later). I suspect that the ":WATER" mask should actually
>> be ":WAT".
>>
>>
>>
>> _______________________________________________
>> 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)
>
>
>
>------------------------------
>
>Message: 3
>Date: Wed, 16 Mar 2016 20:01:55 +0000 (UTC)
>From: Saman Yousuf ali <saman.yousufali64.yahoo.com>
>Subject: Re: [AMBER] rmsd y axis value deviation.
>To: Daniel Roe <daniel.r.roe.gmail.com>, AMBER Mailing List
> <amber.ambermd.org>
>Message-ID:
> <103683198.1058970.1458158515890.JavaMail.yahoo.mail.yahoo.com>
>Content-Type: text/plain; charset=UTF-8
>
>Dear Daniel,Sorry, I have pasted wrong output file. As you told me that due to time 2.0 cpptraj multiplies each frame so I removed time argument from my input file and run rmsd cpptraj command again. I have also run rmsd script with time 10.0 because difference of pico second in each print is 10.0 (ntpr*dt= 5000*0.002= 10.0). Finally, I got the correct value on x-axis 30000 frames in both cases.
>Daniel and Hoeffler, thank you so much both of you for all of your help and guidance.?Best Regards, Saman Yousuf Ali
>
>
> On Thursday, March 17, 2016 12:12 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>
> Hi,
>
>First, the input you posted doesn't correspond to the output. Here's
>the rms command from your input:
>
>On Wed, Mar 16, 2016 at 1:04 PM, Saman Yousuf ali
><saman.yousufali64.yahoo.com> wrote:
>> rms first out rmsd-zinctes.dat @C,CA,N time 10.0
>
>Here is the rms command in your output:
>
>>? 4: [rms first out rmsd-zinctes.dat @C,CA,N time 2.0]
>
>Here you are setting the 'time' argument to 2.0, so cpptraj multiplies
>each frame you have by '2'. Since you have 30000 frames, the final X
>value is 60000.
>
>-Dan
>
>>? ? ? ? Target mask: [.C,CA,N](791)
>>? ? ? ? Reference mask: [.C,CA,N](791)
>> Warning: Coordinates are being rotated and box coordinates are present.
>> Warning: Unit cell vectors are NOT rotated; imaging will not be possible
>> Warning:? after the RMS-fit is performed.
>> ----- itk1.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk2.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk3.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk4.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk5.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk6.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk7.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk8.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk9.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk10.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk11.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk12.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk13.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk14.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk15.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk16.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk17.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk18.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk19.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk20.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk21.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk22.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk23.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk24.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk25.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk26.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk27.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk28.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk29.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> ----- itk30.mdcrd (1-1000, 1) -----
>>? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>>
>> Read 30000 frames and processed 30000 frames.
>> TIME: Trajectory processing: 723.6999 s
>> TIME: Avg. throughput= 41.4536 frames / second.
>>
>> ACTION OUTPUT:
>>
>> DATASETS:
>>? 1 data set:
>>? ? ? ? RMSD_00000 "RMSD_00000" (double, rms), size is 30000
>>
>> DATAFILES:
>>? rmsd-zinctes.dat (Standard Data File):? RMSD_00000
>> ---------- RUN END ---------------------------------------------------
>> TIME: Total execution time: 724.7298 seconds.
>> --------------------------------------------------------------------------------
>> To cite CPPTRAJ use:
>> Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
>>? Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
>>? Theory Comput., 2013, 9 (7), pp 3084-3095.
>> Thank you.
>>? Best Regards, Saman Yousuf Ali
>>
>>
>>? ? On Wednesday, March 16, 2016 4:58 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
>>
>>
>>? On Wed, 16 Mar 2016 11:47:52 +0000
>> Saman Yousuf ali <saman.yousufali64.yahoo.com> wrote:
>>
>>> trajin md_simulation_combine.nc
>>> rms first :1-532.CA,C,N out rmsd.dat
>>> strip :WATER
>>> strip :Na+
>>
>> You are reading a single trajectory file here.? How many frames does it
>> contain, how have you created this file?? Check this first.
>>
>> As far as cpptraj is concerned there is no need to combine trajectories
>> beforehand.? I would recommend to use multiple "trajin" commands to
>> read in the original files.
>>
>> The rms command has an option "time" which you can use to scale the
>> x-axis to your liking.? See the manual.? If you do not use "time" then
>> the x-axis is simply the number of frames.? So why does the file
>> md_simulation_combine.nc have so many?? You originally indicated there
>> should be only half that number.
>>
>> The final "strip" commands don't seem to do anything useful here (unless
>> your script is longer and you do something else with the stripped
>> topology later).? I suspect that the ":WATER" mask should actually
>> be ":WAT".
>>
>>
>>
>> _______________________________________________
>> 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)
>
>
>
>
>------------------------------
>
>Message: 4
>Date: Thu, 17 Mar 2016 08:54:06 +0800 (GMT+08:00)
>From: yhzahsc <yhzahsc.163.com>
>Subject: [AMBER] ???Re: shell script
>To: "AMBER Mailing List" <amber.ambermd.org>
>Message-ID: <687877e8.95f3.1538210b528.Coremail.yhzahsc.163.com>
>Content-Type: text/plain; charset=utf-8
>
>It is working now.
>Thank you!
>
>
>?? ??????
>?2016?03?16? 17:18?Marc van der Kamp ??:
>Hi,
>
>If you get rid of the && at the end of each line, the next job should only start when the job (bash command) before it has finished.
>
>Marc
>
>Sent from my iPhone
>
>> On 16 Mar 2016, at 02:27 am, yhzahsc <yhzahsc.163.com> wrote:
>>
>> Dear Amber List experts,
>> In the TUTORIAL B1: Simulating a small fragment of DNA-Section 6: A Practical Example (A-DNA)?the author use an example script to run all jobs.This makes me want to run all my jobs in a shell script too,however, I have some problems writing a shell script(Amber14). My script is as following:
>>
>>
>> #!/bin/bash
>> mpirun -np 16 sander.MPI -O -i x_min1.in -p x.prmtop -c x.inpcrd -o x_min1.out -r x_min1.rst -ref x.inpcrd &&
>> mpirun -np 16 sander.MPI -O -i x_min2.in -p x.prmtop -c x_min1.rst -o x_min2.out -r x_min2.rst &&
>> mpirun -np 16 sander.MPI -O -i x_md1.in -p x.prmtop -c x_min2.rst -o x_md1.out -r x_md1.rst -x x_md1.mdcrd -ref x_min2.rst &&
>> mpirun -np 16 sander.MPI -O -i x_md2.in -p x.prmtop -c x_md1.rst -o x_md2.out -r x_md2.rst -x x_md2.mdcrd
>>
>>
>> All the commands are executed,but because the first minmizing results,such as ~.rst and ~.out,don't exit,the second command and others produce nothing except for ~.out,which contains nothing.The second command is executed before finishing the first command.
>> How to write the script to run all my jobs in a right way?
>> Thanks.
>> yhz
>> _______________________________________________
>> 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
>
>------------------------------
>
>Message: 5
>Date: Thu, 17 Mar 2016 02:03:10 -0400
>From: Robert Molt <rwmolt07.gmail.com>
>Subject: [AMBER] GROMACS File Conversion Subtlety
>To: AMBER Mailing List <amber.ambermd.org>
>Message-ID: <56EA489E.8020208.gmail.com>
>Content-Type: text/plain; charset=utf-8; format=flowed
>
>Good morning,
>
>I believe I have encountered a bug of sorts in converting an Amber
>trajectory to a GROMACS format...but it's unusual and perhaps very
>limited in its inconvenience.
>
>I converted an Amber trajectory to GROMACS style via cpptraj:
>
>parm name_change.prmtop
>trajin full_no_waters.mdcrd 49990 last 1
>autoimage
>trajout Equilibrated trr
>go
>quit
>
>I can generate a .gro file via the ParmEd version being developed
>currently by Jason Swails on github. When I visualize this in VMD, it
>looks just fine. This is my only meaningful way to check that it works
>correctly, and it passes just fine.
>
>However, when I apply this trajectory to be analyzed using do_x3dna (a
>software developed for analyzing GROMACS trajectories), it fails. After
>consulting with the developer of the do_x3dna software, I find that he
>confirms the trajectory is corrupt in some sense. I eventually tried
>converting the trajectory via VMD, instead of cpptraj, and it worked
>just fine in do_x3dna. The do_x3dna developer confirms using a
>"normally" generated GROMACS .trr file (meaning not coming from Amber,
>originally) works fine.
>
>I do not mean to claim that the conversion in cpptraj does not work most
>generally; it obviously worked fine for me when I checked it visually in
>VMD. Moreover, I am sure this underwent more exhaustive testing that I
>can appreciate. But in some quality, the conversion does not seem to work.
>
>VMD works, but using a GUI is slow (I have many large trajectories). I
>am going to begin experimenting with
>
>http://easybioinfo.free.fr/?q=content/amber-trajectory-gromacs-xtc-conversion
>
>by the esteemed Dr. Lemkul to find a way to do this on the command line.
>
>--
>Dr. Robert Molt Jr.
>r.molt.chemical.physics.gmail.com
>
>
>
>
>------------------------------
>
>Message: 6
>Date: Thu, 17 Mar 2016 08:25:33 +0100
>From: Josh Berryman <the.real.josh.berryman.gmail.com>
>Subject: Re: [AMBER] calculate free energy binding in presence of ions
> witn mmpbsa
>To: AMBER Mailing List <amber.ambermd.org>
>Message-ID:
> <CANRE9HXFiy-AMCFVQXEp48MVaJhbEu0R_mAonuW0=Y+9FksdJg.mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>You could have a look at the conversation that I've been having with Tyler
>and Dave about using 3D RISM for this kind of thing:
>http://archive.ambermd.org/201602/0009.html (your case is simpler than
>mine, in that you are changing ionic species but not pH as far as I
>understand)
>
>also you could consider the EMIL method, which would be valuable in the
>case that you expect some changes to conformation or dynamics of the solute
>as well as just altering the solvation energy via the electrostatics.
>
>tutorial:
>http://ambermd.org/tutorials/advanced/tutorial19/
>
>salt-driven phase transition in DNA:
>http://pubs.acs.org/doi/abs/10.1021/ct3005968
>http://www.sciencedirect.com/science/article/pii/S1875389214002685
>
>
>On 2 March 2016 at 07:48, Carlos Romero <carlos.rom.74he.gmail.com> wrote:
>
>> Hi dear all.
>>
>> Recently I wrote an e-mail for you with respect to calculate free energy
>> binding of a complex in presence of ions.
>>
>> I have been reading a little about it in the amber mailing list and I found
>> in http://archive.ambermd.org/201101/0612.html that there is no way to do
>> what I should try to do.
>>
>> My interest in ions is because I wonder which is the behavior in a
>> Hoffmeiser series in my complex.
>>
>>
>> Does anybody has a suggestion? I will appreciate a lot
>>
>> Thanks in advance
>>
>>
>> Regards
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>------------------------------
>
>Message: 7
>Date: Thu, 17 Mar 2016 16:06:04 +0800 (CST)
>From: jixiaofeng <benniu2004.163.com>
>Subject: [AMBER] errors in plumed and amber14 patch
>To: amber <amber.ambermd.org>
>Message-ID: <59de42a0.bf11.153839c2ecd.Coremail.benniu2004.163.com>
>Content-Type: text/plain; charset=GBK
>
>Dear everyone,
>
>I have installed Amber14 and PLUMED successfully.?I tried to patch amber14 with plumed by typed : plumed patch -p, everything looks OK.
>next? i recompiled the MD code: ./configure gnu & make install. after a long time, the errors occur:
>
>/home/jxf/install/plumed//lib/plumed///src/bias/MetaD.o: In function `int PLMD::Invert<double>(PLMD::Matrix<double> const&, PLMD::Matrix<double>&)':
>MetaD.cpp:(.text._ZN4PLMD6InvertIdEEiRKNS_6MatrixIT_EERNS1_IdEE[int PLMD::Invert<double>(PLMD::Matrix<double> const&, PLMD::Matrix<double>&)]+0x484): undefined reference to `dgetri_'
>MetaD.cpp:(.text._ZN4PLMD6InvertIdEEiRKNS_6MatrixIT_EERNS1_IdEE[int PLMD::Invert<double>(PLMD::Matrix<double> const&, PLMD::Matrix<double>&)]+0x4ef): undefined reference to `dgetri_'
>collect2: ld returned 1 exit status
>make[2]: *** [/home/jxf/software/amber14_back/bin/sander] Error 1
>make[2]: Leaving directory `/home/jxf/software/amber14_back/AmberTools/src/sander'
>make[1]: *** [serial] Error 2
>make[1]: Leaving directory `/home/jxf/software/amber14_back/AmberTools/src'
>make: *** [install] Error 2
>
>the MetaD.cpp, I can find it in : /home/jxf/install/plumed/lib/plumed/src/bias/
>dgetri.f and dgetri.o can be found in /home/jxf/install/lapack-3.6.0/SRC
>
>So, I set the bash file as this :
>####BLAS and LAPACK######
>export LD_LIBRARY_PATH=/home/jxf/install/lapack-3.6.0/SRC:$LD_LIBRARY_PATH
>export LD_LIBRARY_PATH=/home/jxf/install/lapack-3.6.0:$LD_LIBRARY_PATH
>export LD_LIBRARY_PATH=/home/jxf/install/lapack-3.6.0/LAPACKE/src:$LD_LIBRARY_PATH
>######amber14+tool14####
>CC=gcc
>export AMBERHOME="/home/jxf/software/amber14_back"
>export PATH="${PATH}:${AMBERHOME}/bin"
>export LD_LIBRARY_PATH=$AMBERHOME/lib\:$LD_LIBRARY_PATH
>##########plumed#############################
>export PATH=/home/jxf/install/plumed/bin:$PATH
>export INCLUDE_PATH=$INCLUDE_PATH:/home/jxf/install/plumed/include
>export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/jxf/install/plumed/lib
>export PLUMED_KERNEL_PATH=$PLUMED_KERNEL_PATH:/home/jxf/install/plumed/lib/libplumedKernel.so
>export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/jxf/install/plumed/lib/plumed/src/bias/
>
>
>
>how these errors occur?
>
>Thanks and best regards!
>
>Sincerely,
>Xiaofeng Ji
>
>------------------------------
>
>Message: 8
>Date: Thu, 17 Mar 2016 08:41:37 +0000
>From: <hannes.loeffler.stfc.ac.uk>
>Subject: Re: [AMBER] errors in plumed and amber14 patch
>To: <amber.ambermd.org>
>Message-ID:
> <5FF52965BBB9CB46930C7E5D323EC021E6CEB36A.EXCHMBX01.fed.cclrc.ac.uk>
>Content-Type: text/plain; charset="us-ascii"
>
>
>> const&, PLMD::Matrix<double>&)]+0x4ef): undefined reference to `dgetri_'
>> collect2: ld returned 1 exit status
>
>This is the linker complaining that the symbol dgetri_ cannot get resolved (you don't show the relevant command line that was used to link the object files). You need to make sure that the linker uses the proper library for that. I think dgetri is a LAPACK function.
>
>Your shell script does not seem to have any relevant compiled time options.
>
>
>------------------------------
>
>Message: 9
>Date: Thu, 17 Mar 2016 09:50:08 +0100
>From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
>Subject: [AMBER] 2016 ISQBP Meeting: early registration / abstract
> submission deadline approaching
>To: AMBER Mailing List <amber.ambermd.org>
>Message-ID: <56EA6FC0.2080509.mpi-muenster.mpg.de>
>Content-Type: text/plain; charset="utf-8"; format=flowed
>
>Dear colleagues,
>
>The ISQBP President invites in particular young researchers to register
>and submit their abstract for oral presentations at the 2016 *ISQBP2016
>meeting*. The early registration and abstract submission *deadline* for
>*contributed talks* to is in just a few days (*March 20th*). 15 slots
>are available for talks and a particularly advantageous registration
>rate for students is offered.
>
>Registration and abstract submission forms can be found at
>www.isqbp2016.org.
>
>The ISQBP President's Meeting has always been a great networking
>platform for discussing the newest results and developments from diverse
>types of computational approaches to molecular structures.
>
>This time, the program will feature oral presentations by an exciting
>line up of invited speakers:
>Charles L. Brooks III, Thomas E. Cheatham III, Vlad Cojocaru, Annick
>Dejaegere, Carmen Domene, William L. Jorgensen, Syma Khalid, Carmay Lim,
>Alex MacKerell, Lennart Nilsson, Masha Niv, Modesto Orozco, Montgomery
>Pettitt, Carol Post, Rebecca Wade
>
>REGISTRATION FEES: (lunch Mon-Wed, the Welcome Ceremony and the
>Conference Dinner included)
>Student early bird: 2500 nok (ca. 266 euros)
>Student regular price: 3500 nok (ca. 372 euros)
>Regular delegates early bird: 3600 nok (ca. 383 euros)
>Regular delegates after March 20th: 4600 nok (ca. 489 euros)
>
>DATE: 19-22 June 2016
>
>PLACE: Grand Hotel Terminus, Bergen, Norway (www.grandterminus.no/en/).
>The venue is conveniently located in the city center of Bergen, with
>frequent transfer from the airport (30 minutes drive by airport bus or
>taxi).
>
>ACCOMMODATION: rooms at the conference venue or at a nearby hotel can be
>booked via the registration form.
>
>ABSTRACTS: we are welcoming abstracts for ca. 15 short oral
>presentations and posters.
>
>IMPORTANT DATES:
>Early bird registration until March 20th
>Abstract submission deadline for talks: March 20th
>Abstract submission deadline for posters: April 15th
>
>TRAVEL AWARDS: Two ISQBP travel awards will be provided by the Society
>to support students presenting their work at the meeting. The selection
>will be based on the creativity, relevance and quality of the work as
>well as the distance the student has to travel to attend the conference.
>
>MEETING WEBSITE: www.isqbp2016.org <http://www.isqbp2016.org/>
>
>ISQBP: want to know more about the International Society of Quantum
>Biology and Pharmacology? Visit our webpage at http://isqbp.umaryland.edu
>
>
>
>With best regards,
>The Scientific Committee
>
>Nathalie Reuter
>(Computational Biology Unit, University of Bergen)
>
>Bjorn Olav Brandsdal
>(Centre for Theoretical and Computational Chemistry, University of Tromso)
>
>Michele Cascella
>(Centre for Theoretical and Computational Chemistry, University of Oslo)
>
>--
>Dr. Vlad Cojocaru
>Computational Structural Biology Laboratory
>Department of Cell and Developmental Biology
>Max Planck Institute for Molecular Biomedicine
>R?ntgenstrasse 20, 48149 M?nster, Germany
>Tel: +49-251-70365-324; Fax: +49-251-70365-399
>Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
>
>------------------------------
>
>Message: 10
>Date: Thu, 17 Mar 2016 06:02:26 -0400
>From: Jason Swails <jason.swails.gmail.com>
>Subject: Re: [AMBER] errors in plumed and amber14 patch
>To: AMBER Mailing List <amber.ambermd.org>
>Message-ID:
> <CAEk9e3q_LMf6YwLpW7Mb2NBt9qRccrx8M46L+H_YZC5Ej2ARvg.mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>I also highly recommend that you upgrade to AmberTools 15. It is bundled
>with PLUMED support (so there is no need to patch the source code before
>compiling it). It worked great last time I tried it.
>
>HTH,
>Jason
>
>On Thu, Mar 17, 2016 at 4:41 AM, <hannes.loeffler.stfc.ac.uk> wrote:
>
>>
>> > const&, PLMD::Matrix<double>&)]+0x4ef): undefined reference to `dgetri_'
>> > collect2: ld returned 1 exit status
>>
>> This is the linker complaining that the symbol dgetri_ cannot get resolved
>> (you don't show the relevant command line that was used to link the object
>> files). You need to make sure that the linker uses the proper library for
>> that. I think dgetri is a LAPACK function.
>>
>> Your shell script does not seem to have any relevant compiled time options.
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>------------------------------
>
>Message: 11
>Date: Thu, 17 Mar 2016 19:02:29 +0800
>From: Enrique Frio <enrique.frio.gmail.com>
>Subject: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5
> detected"
>To: amber.ambermd.org
>Message-ID:
> <CAOLcVmDyAFpbzeZMhsz5USAurZf+5-1dfH=QNC8MysnOmims9w.mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Hello all,
>
>Amber's current CUDA supported is 7.5, as stated in the main web page,
>right?
>
>I have CUDA Version 7.5.18; single GTX780 (not Ti) GPU.
>
>Amber 14 and Ambertools 15 seem to be failing in installing:
>
>==================================
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>*./configure -cuda gnuChecking for updates...Checking for available patches
>online. This may take a few seconds...Available AmberTools 15 patches:No
>patches availableAvailable Amber 14 patches:No patches availableSearching
>for python2... Found python2.6: /usr/bin/python2.6Error: Unsupported CUDA
>version 7.5 detected. AMBER requires CUDA version == 5.0 .or. 5.5
>.or. 6.0 .or. 6.5Configure failed due to the errors above!*
>==================================
>
>Your assistance will be much appreciated. :)
>
>--
>Cheers,
>Enrique
><http://www.rbc.org/odb/odb.shtml>
>
>
>------------------------------
>
>Message: 12
>Date: Thu, 17 Mar 2016 13:03:51 +0000
>From: anu chandra <anu80125.gmail.com>
>Subject: Re: [AMBER] Error with make test.parallel in AmberTools 15
> installation
>To: AMBER Mailing List <amber.ambermd.org>
>Message-ID:
> <CADEHHNnbK3Zst1TyaGBHBsob-X6tsX0U0UXUXpaZCuTu9m3-gQ.mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Hi,
>
>Thanks for the reply Daniel. The details of the installation are follows,
>
>$ ./configure -mpi --with-python /usr/bin/python2.7 gnu - used for
>configuring Amber
>
>Then,
>
>$ make install - used for installation
>
>
>gcc version
>
>$ gcc -v
>Using built-in specs.
>COLLECT_GCC=gcc
>COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
>Target: x86_64-redhat-linux
>Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
>--infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla
>--enable-bootstrap --enable-shared --enable-threads=posix
>--enable-checking=release --with-system-zlib --enable-__cxa_atexit
>--disable-libunwind-exceptions --enable-gnu-unique-object
>--enable-linker-build-id --with-linker-hash-style=gnu
>--enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto
>--enable-plugin --enable-initfini-array --disable-libgcj
>--with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install
>--with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install
>--enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64
>--build=x86_64-redhat-linux
>Thread model: posix
>gcc version 4.8.5 20150623 (Red Hat 4.8.5-4) (GCC)
>
>
>MPI details
>
>$ mpicc -show
>cc -m64 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>-fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches
>-m64 -mtune=generic -fPIC -Wl,-z,noexecstack -I/usr/include/mpich-x86_64
>-L/usr/lib64/mpich/lib -Wl,-rpath -Wl,/usr/lib64/mpich/lib -lmpich -lopa
>-lmpl -lrt -lpthread
>
>$ mpif90 -show
>gfortran -m64 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>-fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches
>-m64 -mtune=generic -fPIC -Wl,-z,noexecstack -I/usr/include/mpich-x86_64
>-I/usr/include/mpich-x86_64 -L/usr/lib64/mpich/lib -lmpichf90 -Wl,-rpath
>-Wl,/usr/lib64/mpich/lib -lmpich -lopa -lmpl -lrt -lpthread
>
>
>
>Many thanks
>Anu
>
>
>On Wed, Mar 16, 2016 at 4:32 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> Have all updates been applied? How was Amber configured (what flags
>> were used), what compilers and version, and what MPI and version are
>> in use?
>>
>> -Dan
>>
>> On Wed, Mar 16, 2016 at 10:28 AM, anu chandra <anu80125.gmail.com> wrote:
>> > Dear Amber users,
>> >
>> > While doing make test.parallel after installing AmberTools 15, I
>> > experienced the following error. I have set export DO_PARALLEL='mpirun
>> -np
>> > 2' , before doing the test. Any help would be highly appreciated
>> >
>> >
>> >
>> *****************************************************************************************************************************************
>> > make[2]: Target `test.parallel.at' not remade because of errors.
>> > make[2]: Leaving directory `/usr/local/amber14/test'
>> > make[2]: Entering directory `/usr/local/amber14/AmberTools/test'
>> >
>> > Finished test suite for AmberTools at Wed Mar 16 16:15:19 GMT 2016.
>> >
>> > make[2]: Leaving directory `/usr/local/amber14/AmberTools/test'
>> > 370 file comparisons passed
>> > 2 file comparisons failed
>> > 60 tests experienced errors
>> > Test log file saved as
>> > /usr/local/amber14/logs/test_at_parallel/2016-03-16_15-58-10.log
>> > Test diffs file saved as
>> > /usr/local/amber14/logs/test_at_parallel/2016-03-16_15-58-10.diff
>> > make[1]: Leaving directory `/usr/local/amber14/AmberTools/test'
>> > ==============================================================
>> > /usr/local/amber14/src/Makefile not found.
>> > This is expected if you have not installed Amber14.
>> > ==============================================================
>> >
>> >
>> ***************************************************************************************************************************************
>> >
>> >
>> > Part of the
>> > /usr/local/amber14/logs/test_at_parallel/2016-03-16_15-58-10.log is shown
>> > below,
>> >
>> >
>> >
>> >
>> **************************************************************************************************************************************
>> > export TESTsander=/usr/local/amber14/bin/sander.MPI; cd jar_multi &&
>> > ./Run.jarz
>> >
>> > Running multisander version of sander Amber14
>> > Total processors = 2
>> > Number of groups = 2
>> >
>> >
>> > Program received signal SIGSEGV: Segmentation fault - invalid memory
>> > reference.
>> >
>> > Backtrace for this error:
>> > #0 0x7F482577D467
>> > #1 0x7F482577DAAE
>> > #2 0x7F4824C8466F
>> > #3 0x7F482583ABE8
>> > #4 0x5C1C51 in amopen_ at amopen.F90:90 (discriminator 1)
>> > #5 0x508FD7 in mdread1_ at mdread1.F90:182
>> > #6 0x4D6159 in sander_ at sander.F90:326
>> > #7 0x4D4E12 in multisander at multisander.F90:436
>> >
>> >
>> ===================================================================================
>> > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> > = EXIT CODE: 139
>> > = CLEANING UP REMAINING PROCESSES
>> > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>> >
>> ===================================================================================
>> > YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>> > (signal 11)
>> > This typically refers to a problem with your application.
>> > Please see the FAQ page for debugging suggestions
>> > ./Run.jarz: Program error
>> > make[2]: [test.sander.BASIC.MPI] Error 1 (ignored)
>> > export TESTsander=/usr/local/amber14/bin/sander.MPI; cd ti_eth2meth_gas
>> &&
>> > ./Run.test1
>> >
>> > Running multisander version of sander Amber14
>> > Total processors = 2
>> > Number of groups = 2
>> >
>> >
>> > Program received signal SIGSEGV: Segmentation fault - invalid memory
>> > reference.
>> >
>> > Backtrace for this error:
>> > #0 0x7FBD4B1CB467
>> > #1 0x7FBD4B1CBAAE
>> > #2 0x7FBD4A6D266F
>> > #3 0x7FBD4B288BE8
>> > #4 0x5C1C51 in amopen_ at amopen.F90:90 (discriminator 1)
>> > #5 0x508FD7 in mdread1_ at mdread1.F90:182
>> > #6 0x4D6159 in sander_ at sander.F90:326
>> > #7 0x4D4E12 in multisander at multisander.F90:436
>> >
>> >
>> ===================================================================================
>> > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> >
>> >
>> >
>> **************************************************************************************************************************************************
>> > _______________________________________________
>> > 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
>>
>
>
>------------------------------
>
>Message: 13
>Date: Thu, 17 Mar 2016 07:37:19 -0600
>From: Daniel Roe <daniel.r.roe.gmail.com>
>Subject: Re: [AMBER] GROMACS File Conversion Subtlety
>To: AMBER Mailing List <amber.ambermd.org>
>Message-ID:
> <CAAC0qOZGP3Xoe_EUMvMhfzKzKUfA0e34AzMh6acJ9PxG17866A.mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Hi Robert,
>
>Thanks for bringing this to my attention. I don't often work with
>gromacs files so it's certainly possible there is some issue with
>cpptraj-generated trr files. I have checked them with VMD as well and
>found no probelsm (i.e. vmd reads cpptraj-generated trr files just
>fine) so its likely something subtle with the format as you suggest.
>What version of cpptraj did you run this with? And can you provide any
>more details on what the error was (exact message(s), segfault, etc)?
>I'll look into this and see what I can find.
>
>-Dan
>
>
>On Thu, Mar 17, 2016 at 12:03 AM, Robert Molt <rwmolt07.gmail.com> wrote:
>> Good morning,
>>
>> I believe I have encountered a bug of sorts in converting an Amber
>> trajectory to a GROMACS format...but it's unusual and perhaps very
>> limited in its inconvenience.
>>
>> I converted an Amber trajectory to GROMACS style via cpptraj:
>>
>> parm name_change.prmtop
>> trajin full_no_waters.mdcrd 49990 last 1
>> autoimage
>> trajout Equilibrated trr
>> go
>> quit
>>
>> I can generate a .gro file via the ParmEd version being developed
>> currently by Jason Swails on github. When I visualize this in VMD, it
>> looks just fine. This is my only meaningful way to check that it works
>> correctly, and it passes just fine.
>>
>> However, when I apply this trajectory to be analyzed using do_x3dna (a
>> software developed for analyzing GROMACS trajectories), it fails. After
>> consulting with the developer of the do_x3dna software, I find that he
>> confirms the trajectory is corrupt in some sense. I eventually tried
>> converting the trajectory via VMD, instead of cpptraj, and it worked
>> just fine in do_x3dna. The do_x3dna developer confirms using a
>> "normally" generated GROMACS .trr file (meaning not coming from Amber,
>> originally) works fine.
>>
>> I do not mean to claim that the conversion in cpptraj does not work most
>> generally; it obviously worked fine for me when I checked it visually in
>> VMD. Moreover, I am sure this underwent more exhaustive testing that I
>> can appreciate. But in some quality, the conversion does not seem to work.
>>
>> VMD works, but using a GUI is slow (I have many large trajectories). I
>> am going to begin experimenting with
>>
>> http://easybioinfo.free.fr/?q=content/amber-trajectory-gromacs-xtc-conversion
>>
>> by the esteemed Dr. Lemkul to find a way to do this on the command line.
>>
>> --
>> Dr. Robert Molt Jr.
>> r.molt.chemical.physics.gmail.com
>>
>>
>> _______________________________________________
>> 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)
>
>
>
>------------------------------
>
>Message: 14
>Date: Thu, 17 Mar 2016 08:02:24 -0700
>From: Ross Walker <ross.rosswalker.co.uk>
>Subject: Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5
> detected"
>To: AMBER Mailing List <amber.ambermd.org>
>Message-ID: <57A2DB8D-2AF2-43B0-8B1C-279E6E89B51C.rosswalker.co.uk>
>Content-Type: text/plain; charset=us-ascii
>
>Hi Enrique
>
>You did not apply the latest updates - or rather the updates failed to be applied. Try:
>
>cd $AMBERHOME
>./update_amber --update
>
>Then try again. If that does not work then something is messed up your AMBER installation. I would suggest going back to the original tar files and trying again, saying yes to all updated.
>
>All the best
>Ross
>
>> On Mar 17, 2016, at 04:02, Enrique Frio <enrique.frio.gmail.com> wrote:
>>
>> Hello all,
>>
>> Amber's current CUDA supported is 7.5, as stated in the main web page,
>> right?
>>
>> I have CUDA Version 7.5.18; single GTX780 (not Ti) GPU.
>>
>> Amber 14 and Ambertools 15 seem to be failing in installing:
>>
>> ==================================
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *./configure -cuda gnuChecking for updates...Checking for available patches
>> online. This may take a few seconds...Available AmberTools 15 patches:No
>> patches availableAvailable Amber 14 patches:No patches availableSearching
>> for python2... Found python2.6: /usr/bin/python2.6Error: Unsupported CUDA
>> version 7.5 detected. AMBER requires CUDA version == 5.0 .or. 5.5
>> .or. 6.0 .or. 6.5Configure failed due to the errors above!*
>> ==================================
>>
>> Your assistance will be much appreciated. :)
>>
>> --
>> Cheers,
>> Enrique
>> <http://www.rbc.org/odb/odb.shtml>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>------------------------------
>
>Message: 15
>Date: Thu, 17 Mar 2016 16:02:56 +0100
>From: Thomas Exner <thomas.exner.uni-konstanz.de>
>Subject: [AMBER] Training and Innovation Course in Drug Design
>To: AMBER Mailing List <amber.ambermd.org>
>Message-ID: <56EAC720.8040401.uni-konstanz.de>
>Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
> Training and Innovation Course in Drug Design
>
>
> Mon, 18. Jul. to Fri, 22. Jul. 2016
>
>
> Department of Pharmaceutical Sciences, University of Milano
>
>We like to invite you to a one-week hands-on workshop on methods and
>tools in rational drug design co-organized by the Department of
>Pharmaceutical Science and eChemInfo.
>
><http://www.echeminfo.com/events/drug-design-euro-2016>http://www.echeminfo.com/events/drug-design-euro-2016
>
>This workshop will provide a set of *stimulating lectures and group work
>sessions* using state-of-the-art and emerging modelling techniques of
>relevance to chemists, life scientists and modellers working in rational
>drug design. Participants should return to their labs with *new ideas,
>best practices and software experiences* to maximise productivity in
>their own drug discovery research activities.
>
>Main topics covered are: virtual screening, ligand-based and
>structure-based drug design, bio- and cheminformatics, molecular
>dynamics simulation, drug delivery modelling, systems biology and
>biotech drug design. The functionalities of tools developed in academic
>groups and from the main software providers will be explored based on
>tutorials and more important on case studies taken from ongoing research.
>
>Use the ?*bring your own problems?* option to directly apply your newly
>acquired knowledge to your own research, profit from specific advice by
>the experts and other participants and contribute to innovative
>approaches for all case studies.
>
>*Bursary Awards are available, deadline was extended until 31 March at
>*<http://www.echeminfo.com/bursary-awards>http://www.echeminfo.com/bursary-awards**
>
>*Early-bird reduced rates until 31 March*
>
>For further information and questions on these and other eChemInfo
>workshops, please visit _http://www.echeminfo.com/events_or contact us.
>
>Alessandro ContiniThomas Exner
>University of Milano Douglas Connect
>
>
>
>------------------------------
>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
>
>
>End of AMBER Digest, Vol 1518, Issue 1
>**************************************
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 17 2016 - 19:30:05 PDT
