Re: [AMBER] ASMD equil4 not producing output files

From: Hantz, Eric R. <hantz.2.buckeyemail.osu.edu>
Date: Wed, 29 Jul 2020 20:11:18 +0000

Hello,

I was able to work around my issue by utilizing gpus for the last equilibration step. I believe the issue was that while only running on cpus I did not give sufficient walltime for enough steps to be performed to write to the output files. Everything is running smoothly now.


 
Eric Hantz
Biophysics Graduate Program
Lindert Lab
2120 Newman Wolfrom
 

´╗┐On 7/28/20, 3:00 PM, "amber-request.ambermd.org" <amber-request.ambermd.org> wrote:

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    AMBER Mailing List Digest
    
    Today's Topics:
    
       1. Re: Error building Amber (Walton Smith)
       2. Problems generating charges with RESP (Lucas Bandeira)
       3. Problem installing AmberMD with MPI support on Cray XC40
          (Jakub Jalowiec)
       4. Re: Amber20 Compiling problem with b2 and Boost.Regex
          (Amanda Buyan)
       5. Problems deriving charges with RESP (Lucas Bandeira)
       6. Re: Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???)
       7. Re: Error building Amber (Gustaf Olsson)
       8. Re: Error building Amber (David A Case)
       9. ASMD equil4 not producing output files (Hantz, Eric R.)
      10. Re: Issue about "... . RESTARTED DUE TO LINMIN FAILURE..."
          (David A Case)
      11. Re: Error building Amber (Walton Smith)
      12. Tracking lifetime distance by closest of specific water IDs?
          (Kenneth Huang)
      13. Re: Interaction of cellulose-hemicellulose (Pinky Mazumder)
      14. Re: ASMD equil4 not producing output files (Adrian Roitberg)
      15. Issue heating system in equilibration step (Samuel A. Ratliff)
      16. AMD parameter: protein residue should count ligand or not
          (Lod King)
    
    
    ----------------------------------------------------------------------
    
    Message: 1
    Date: Mon, 27 Jul 2020 15:50:54 -0400
    From: Walton Smith <smit7450.mylaurier.ca>
    Subject: Re: [AMBER] Error building Amber
    To: AMBER Mailing List <amber.ambermd.org>
    Message-ID: <0E5FDC7E-E18F-453C-BCE7-3C738461779A.mylaurier.ca>
    Content-Type: text/plain; charset="utf-8"
    
    Hey Dac,
    
    I?m using Catalina (10.15.5), and I do have homebrew from when I installed the open source PyMOL. In my /usr/local/lib folder I have cmake, docker, python3.7 and python 3.8 along with an unknown pkgconfig folder and several lib?.dylib and .a files. I have attached the cmake.log file. Let me know if you might have any idea. Thank you so much for getting back to me so fast.
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    WS
    
> On Jul 27, 2020, at 1:48 PM, David A Case <david.case.rutgers.edu> wrote:
>
> On Mon, Jul 27, 2020, Walton Smith wrote:
>>
>>
>> I?m having trouble with building AMBER. After I ./run_cmake in terminal,
>> the configuration never runs to completion. Here is the error log and
>> output log associated with my difficulties. Please let me know what I can
>> do to fix this issue, I would greatly appreciate it. Just to let you know,
>> I?m not very familiar with terminal so this is all pretty new to me.
>
> It's best to post the "cmake.log" file that is created by run_cmake.
>
> Also, let us know about your operating system and configuration. It
> looks like you are using OSX, but which version? and is there anything
> odd about your setup (is homebrew or something like that installed)?
> What do you have (if anything) in your /usr/local/lib folder?
>
> ...thanks....dac
>
>
> _______________________________________________
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    ------------------------------
    
    Message: 2
    Date: Mon, 27 Jul 2020 17:39:01 -0300
    From: Lucas Bandeira <bandeiralucas97.gmail.com>
    Subject: [AMBER] Problems generating charges with RESP
    To: AMBER Mailing List <amber.ambermd.org>
    Message-ID:
            <CAM1=HZnnyxmis-kivyS4AY=-7g=r_Ng4EG6hqbwtRi3njyirHw.mail.gmail.com>
    Content-Type: text/plain; charset="utf-8"
    
    Dear AMBER Community,
    
    I'm using RESP to derivate charges for a non-standard residue. I'm
    following this tutorial (
    https://urldefense.com/v3/__https://ambermd.org/tutorials/advanced/tutorial1/section1.htm__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7C_v52-KQ$ ). I had
    problems when reading the charges to be constrained to the caps from the
    qin file: the charges in the qout_stage2 file for the constrained atoms are
    not equal to the specified in the qin file. Also, degenerate atoms have
    different charges. Could someone help me to solve this?
    
    I'm sending in attachment the qin.dat, the .ac, the .pdb, and the resp
    input and output files. The cap I'm using is methanol.
    
    Yours faithfully,
    
    Lucas Bandeira
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    ------------------------------
    
    Message: 3
    Date: Tue, 28 Jul 2020 00:27:13 +0200
    From: Jakub Jalowiec <jj358817.icm.edu.pl>
    Subject: [AMBER] Problem installing AmberMD with MPI support on Cray
            XC40
    To: Amber <amber.ambermd.org>
    Message-ID: <88282eb0b488422a268758a87f6d505b.icm.edu.pl>
    Content-Type: text/plain; charset=US-ASCII; format=flowed
    
    Dear Amber community,
    I am trying to compile AmberMD with the -mpi flag enabled on an Intel
    Haswell Cray XC40 using Cray compilers. I am using MPICH
    (cray-mpich/7.7.10). Take a look at my compilers:
    
> jj358817.nid00392:~/MM/amber/amber/amber20_src/build> which cc
> /opt/cray/pe/craype/2.6.1/bin/cc
> jj358817.nid00392:~/MM/amber/amber/amber20_src/build> which CC
> /opt/cray/pe/craype/2.6.1/bin/CC
> jj358817.nid00392:~/MM/amber/amber/amber20_src/build> which ftn
> /opt/cray/pe/craype/2.6.1/bin/ftn
    
    Moreover cc, CC and ftn are all MPI wrappers (i.e. I can compile MPI
    code using them just fine).
    
    The cmake flags I'm using (amber20_src/build/run_cmake) look like this
    (as far as I understand I had to pass -DMPI_C_LIBRARIES and
    -DMPI_C_INCLUDE_PATH to MPICH directories so cc, CC and ftn are properly
    recognised as MPI wrappers):
    
> cmake $AMBER_PREFIX/amber20_src \
> -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20 \
> -DCOMPILER=CRAY \
> -DMPI=TRUE -DCUDA=FALSE -DINSTALL_TESTS=TRUE
> -DMPI_C_LIBRARIES=/opt/cray/pe/mpt/7.7.10/gni/mpich-crayclang/9.0/lib/
> -DMPI_C_INCLUDE_PATH=/opt/cray/pe/mpt/7.7.10/gni/mpich-crayclang/9.0/include/
> \
> -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE
> -DCMAKE_VERBOSE_MAKEFILE=TRUE \
> 2>&1 | tee cmake.log
    
    When I do ./run_cmake in that directory I get:
> jj358817.nid00392:~/MM/amber/amber/amber20_src/build> ./run_cmake
> --
> **************************************************************************
> -- Starting configuration of Amber version 20.0.0...
> -- CMake Version: 3.10.2
> -- For how to use this build system, please read this wiki:
> -- https://urldefense.com/v3/__http://ambermd.org/pmwiki/pmwiki.php/Main/CMake__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7CrwMX7Eg$
> -- For a list of important CMake variables, check here:
> -- https://urldefense.com/v3/__http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7BtQV0vzw$
> --
> **************************************************************************
> -- Amber source not found, only building AmberTools
> -- Cray Programming Environment 2.6.1 Fortran
> -- Testing if stdlib.h can be included...
> -- Testing if stdlib.h can be included... yes
> WARNING: Target "cmTC_e0684" requests linking to directory
> "/opt/cray/pe/mpt/7.7.10/gni/mpich-crayclang/9.0/lib/". Targets may
> link only to libraries. CMake is dropping the item.
> -- MPI C Compiler: /opt/cray/pe/craype/2.6.1/bin/cc
> -- MPI CXX Compiler: /opt/cray/pe/craype/2.6.1/bin/CC
> -- MPI Fortran Compiler: /opt/cray/pe/craype/2.6.1/bin/ftn
> -- If these are not the correct MPI wrappers, then set
> MPI_<language>_COMPILER to the correct wrapper and reconfigure.
> CMake Error at cmake/LibraryTracking.cmake:174 (message):
> Incorrect usage. At least one LIBRARY should be provided.
> Call Stack (most recent call first):
> cmake/MPIConfig.cmake:122 (import_libraries)
> CMakeLists.txt:118 (include)
    
    The error message "Incorrect usage. At least one LIBRARY should be
    provided." is undescriptive. :( I tried to hunt down the cause of that
    error by myself trying to debug cmake/LibraryTracking.cmake but failed
    as I am new to CMake. I am stuck now. Can you please guide me in
    resolving that problem?
    
    Best regards,
    Jakub
    
    
    
    ------------------------------
    
    Message: 4
    Date: Mon, 27 Jul 2020 22:50:37 +0000
    From: Amanda Buyan <Amanda.Buyan.anu.edu.au>
    Subject: Re: [AMBER] Amber20 Compiling problem with b2 and Boost.Regex
    To: AMBER Mailing List <amber.ambermd.org>, "david.case.rutgers.edu"
            <david.case.rutgers.edu>
    Message-ID:
            <SYBP282MB0202CF54191083BC924FA24FA9720.SYBP282MB0202.AUSP282.PROD.OUTLOOK.COM>
            
    Content-Type: text/plain; charset="us-ascii"
    
    Hi DAC,
    
    I just checked, and I've got cmake in my path (under /usr/local/bin, which I have added to my PATH in my .bashrc file, and I had to add it in the run_cmake as well). It's also version 3.14.5, if that helps.
    
    Best wishes
    
    Amanda
    ________________________________
    From: David A Case <david.case.rutgers.edu>
    Sent: 27 July 2020 23:10
    To: AMBER Mailing List <amber.ambermd.org>
    Subject: Re: [AMBER] Amber20 Compiling problem with b2 and Boost.Regex
    
    On Mon, Jul 27, 2020, Amanda Buyan wrote:
>
>I'm currently having trouble with compiling even the serial version of
>Amber20 on the second cluster of ours. When I run the "make install"
>command (following the same procedure as on the other cluster), I get the
>following error:
>
>---
>Building Boost.Build engine with toolset gcc... tools/build/src/engine/bin.linuxx86_64/b2
>Detecting Python version... 3.6
>Detecting Python root... /usr
>Unicode/ICE support for Boost.Regex?... not foud.
>Generating Boost.Build configuration in project-config.jam...
>
>Bootstrapping is done. To build, run:
>
>./b2
>
>to adjust configuration, edit 'project-config.jam'.
>
>[ Further information about boost.build]
>
>/bin/sh: cmake: command not found
    
    I think this is the problem: you have to have cmake in your PATH: it's not
    enough to just specify the location in the run_cmake script.
    
    This is not documented in our installation instructions. And, it might not be
    the only problem. But check on the second cluster to see if cmake is in your
    PATH.
    
    ...dac
    
    
    _______________________________________________
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    AMBER.ambermd.org
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    ------------------------------
    
    Message: 5
    Date: Mon, 27 Jul 2020 21:23:52 -0300
    From: Lucas Bandeira <bandeiralucas97.gmail.com>
    Subject: [AMBER] Problems deriving charges with RESP
    To: AMBER Mailing List <amber.ambermd.org>
    Message-ID:
            <CAM1=HZkdgkVoCMca1a6bZuzoGjsr5DMWZ-=MauZm78V6rchdGg.mail.gmail.com>
    Content-Type: text/plain; charset="utf-8"
    
    Dear AMBER Community,
    
    When I try to generate charges using RESP I have the following message in
    the step1.respout1 file:
    
     Non-linear optimization requested.
     chgopt: LU decomp gave almost-singular U Non-linear optimization requested.
    
    Another thing that does not seems right is this line:
    
    total number of atoms = 14
    
    The molecule has 144 atoms.
    
    I'm sending in attachment the resp input and output files, and the qin
    files for restraining charge values.
    
    Yours faithfully,
    
    Lucas Bandeira
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    ------------------------------
    
    Message: 6
    Date: Tue, 28 Jul 2020 09:48:41 +0800 (GMT+08:00)
    From: ??? <xzhfood.njau.edu.cn>
    Subject: Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN
            FAILURE..."
    To: amber.ambermd.org
    Message-ID: <73e2cc95.2e09f.173931b87de.Coremail.xzhfood.njau.edu.cn>
    Content-Type: text/plain; charset=UTF-8
    
    Thank you David,
    I process the box boundry using equil trajectory mdcrd file to generate a correspoding nc file due to a partition of water moleculare out of box after equilation, and then open the nc file in the vmd, and select parameters "save coordinate,fist 499, last 499, stride 1" and save as DLF-equil-499.pdb file as QM/MM inuptfile (but box is gone from here) when the runing box stop, and then a new prmtop and incrd were generated from DLF-equil-499.pdb, I presume this is the case where the issue occured, but I do not know how to fix the issue, please help me, thank you.
    
    Process the box boundry file re_image.in
    _________________________
    parm DLFae4-MFA-complex-wat.prmtop
    
    trajin DLFae4-MFA_equil.mdcrd
    
    center :1-339
    
    image center familiar
    
    trajout DLFae4-MFA-wat_equil_reimaged.nc
    _________________________________________
    
    cpptraj -i re_image.in
    
    
    a new prmtop and incrd file generating file
    
    ---------------------------------------------------
    tleap -f oldff/leaprc.ff99SB
     
>source leaprc.gaff
>source leaprc.water.tip3p
>loadamberparams MFA.frcmod ?ligand?
>loadoff MFA.lib
>com = loadpdb DLF-equil-499.pdb
> charge com
> addions com Na+ 0
> saveamberparm com DLF-equil-499.prmtop DLF-equil-499.inpcrd
> quit
    
    -------------------------------------------------------
    
    Zhihong Xin
    
    
> -----Original Messages-----
> From: amber-request.ambermd.org
> Sent Time: 2020-07-28 03:00:01 (Tuesday)
> To: amber.ambermd.org
> Cc:
> Subject: AMBER Digest, Vol 3076, Issue 1
>
> Send AMBER mailing list submissions to
> amber.ambermd.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7ADQUNa8w$
> or, via email, send a message with subject or body 'help' to
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>
> You can reach the person managing the list at
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>
> 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: Issue about "... . RESTARTED DUE TO LINMIN FAILURE..."
> (David A Case)
> 2. Re: Maximum system size (David A Case)
> 3. Amber20 Compiling problem with b2 and Boost.Regex (Amanda Buyan)
> 4. Charges for modified DNA base at the termini? (Kenneth Huang)
> 5. Re: Amber20 Compiling problem with b2 and Boost.Regex
> (David A Case)
> 6. Error building Amber (Walton Smith)
> 7. Re: Error building Amber (David A Case)
> 8. Re: Error building Amber (David A Case)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 26 Jul 2020 20:44:15 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN
> FAILURE..."
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20200727004415.mlqxwocrdmxpvyix.pop-os.localdomain>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> On Sun, Jul 26, 2020, ??? wrote:
> >
> >I extract the last frame (499 frames) of the equil pdb outfile as the
> >QM-MM input file, and regenerate prmtop and Inpcrd file, but I found that
> >the BOX coordinates in the inpcrd file are gone,
>
> Something went wrong here, and you should investigate. You don't say how you
> extracted the last frame, nor how you regenerated the prmtop and incrd file.
>
> But if you do that correctly, the box information should not be lost.
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 26 Jul 2020 20:57:50 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Maximum system size
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20200727005750.oa4uunwn44luzetz.pop-os.localdomain>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Sun, Jul 26, 2020, Jack Shepherd wrote:
> >
> >Making a big system for simulation with pmemd.cuda recently I got the
> >error c must be smaller than 10^4 angstroms and nfft3 must be between
> >certain values.
>
> The maximum value for nfft1,2,3 is hard-coded in mdin_ewald_dat.F90 (see the
> gridhi variable), and the maximum box size is in boxhi (as 1000. Ang, not
> 10000 Ang., and least as I read the code.)
>
> I know that people have doubled the gridhi value, and you might experiment
> with making gridhi and boxhi larger. I'm not sure how these values will
> carry over to pmemd.cuda, but you can experiment: run short simulations with
> CPU first, then make sure you get equivalent results on the GPU.
>
> Once you get a very big system volume, the number of atoms is likely to become
> more of a limitation than is the size of the box or the number of PME grid
> points. Don't expect this to be straightforward: a cubic box of water
> with sides of 1000 Ang. would have 33 million molecules, or 100 million atoms.
> This is well beyond the expected range of Amber simulations, and generally
> requires both specialized hardware and software.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 27 Jul 2020 01:35:07 +0000
> From: Amanda Buyan <Amanda.Buyan.anu.edu.au>
> Subject: [AMBER] Amber20 Compiling problem with b2 and Boost.Regex
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <SYBP282MB020247875ADC0D20EC5644E2A9720.SYBP282MB0202.AUSP282.PROD.OUTLOOK.COM>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi everyone,
>
> Thanks for your suggestion on removing the PLUMED library - it helped! I have another question, as I'm installing Amber20 on multiple clusters:
>
> I'm currently having trouble with compiling even the serial version of Amber20 on the second cluster of ours. When I run the "make install" command (following the same procedure as on the other cluster), I get the following error:
>
> ---
> Building Boost.Build engine with toolset gcc... tools/build/src/engine/bin.linuxx86_64/b2
> Detecting Python version... 3.6
> Detecting Python root... /usr
> Unicode/ICE support for Boost.Regex?... not foud.
> Generating Boost.Build configuration in project-config.jam...
>
> Bootstrapping is done. To build, run:
>
> ./b2
>
> to adjust configuration, edit 'project-config.jam'.
>
> [ Further information about boost.build]
>
> /bin/sh: cmake: command not found
> make[2]: *** [AmberTools/src/boost/Stamp/boost_build/boost_build-bootstrap] Error 127
> make[1]: *** [AmberTools/src/boost/CMakeFiles/boost_build.dir/all] Error 2
> make: *** [all] Error 2
> ---
>
> I try to find the program b2, but I can't find any installation for it (it might have been on the other cluster, but I'm not sure). How do I check this? Do you have any advice on how to get past this step?
>
> Thanks in advance for your help.
>
> Best wishes
>
> Amanda
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 27 Jul 2020 02:50:39 -0400
> From: Kenneth Huang <kennethneltharion.gmail.com>
> Subject: [AMBER] Charges for modified DNA base at the termini?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CALeh7kCs9D6bzk=OYrq5QZkqDxO2fEAjOrQScUE6R+y74XpKPg.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi all,
>
> Something of a procedural/background question- what is the exact procedure
> for determining the charges for modified/unnatural bases at the 5'/3'
> termini?
>
> Given the termini are unique, ie their charge is non-integer by design, the
> closest I could find is the tutorial here (
> https://urldefense.com/v3/__https://ambermd.org/tutorials/advanced/tutorial1/section1.htm__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7C_v52-KQ$ ), but trying
> to follow it as close as possible in AmberTools16 with a test run of
> something simple of native DG3' nets an EOF runtime error-
>
> resp -O -i dg_resp.in -o dg_resp.out -p dg_resp.pch -t dg_resp.chg -q
> > dg-resp1.qin -e dg_esp1.esp
> > At line 744 of file resp.F (unit = 5, file = 'dg_resp.in')
> > Fortran runtime error: End of file
> >
>
> Which I've figured has something to do with how my group constraints are
> formatted?
>
> ...etc
> > 1 0
> > 34 -0.6921
> > 1 1 1 2 1 3 1 4 1 5 1 6 1 7
> > 1 8
> > 1 9 1 10 1 11 1 12 1 13 1 14 1 15
> > 1 16
> > ...etc
> >
>
> But I can't see anything that's obviously wrong about it, or did I
> misunderstand how the group constraint is meant to work?
>
> Or am I going about this the entirely wrong way? I know in the case of DNA
> forcefields, the charges have been relatively fixed since ff94/99- so could
> I approach it as an internal base, ie do the ESP/RESP fitting on just the
> modified base portion with a methyl cap, and 'stitch' the backbone/sugar
> from the source forcefield back together for a complete base?
>
>
> Best,
>
> Kenneth
>
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 27 Jul 2020 09:10:37 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Amber20 Compiling problem with b2 and Boost.Regex
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20200727131037.waj5o5yims736ped.pop-os.localdomain>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Mon, Jul 27, 2020, Amanda Buyan wrote:
> >
> >I'm currently having trouble with compiling even the serial version of
> >Amber20 on the second cluster of ours. When I run the "make install"
> >command (following the same procedure as on the other cluster), I get the
> >following error:
> >
> >---
> >Building Boost.Build engine with toolset gcc... tools/build/src/engine/bin.linuxx86_64/b2
> >Detecting Python version... 3.6
> >Detecting Python root... /usr
> >Unicode/ICE support for Boost.Regex?... not foud.
> >Generating Boost.Build configuration in project-config.jam...
> >
> >Bootstrapping is done. To build, run:
> >
> >./b2
> >
> >to adjust configuration, edit 'project-config.jam'.
> >
> >[ Further information about boost.build]
> >
> >/bin/sh: cmake: command not found
>
> I think this is the problem: you have to have cmake in your PATH: it's not
> enough to just specify the location in the run_cmake script.
>
> This is not documented in our installation instructions. And, it might not be
> the only problem. But check on the second cluster to see if cmake is in your
> PATH.
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 27 Jul 2020 10:04:33 -0400
> From: Walton Smith <smit7450.mylaurier.ca>
> Subject: [AMBER] Error building Amber
> To: amber.ambermd.org
> Message-ID: <3A1E27EB-7D19-46E4-B5DB-814F47518094.mylaurier.ca>
> Content-Type: text/plain; charset="utf-8"
>
> Hello,
>
> I?m having trouble with building AMBER. After I ./run_cmake in terminal, the configuration never runs to completion. Here is the error log and output log associated with my difficulties. Please let me know what I can do to fix this issue, I would greatly appreciate it. Just to let you know, I?m not very familiar with terminal so this is all pretty new to me.
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 7
> Date: Mon, 27 Jul 2020 13:15:14 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Error building Amber
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20200727171514.m22a4eqpjexzyy7o.oq-fs-191g302-a.rad.rutgers.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> On Mon, Jul 27, 2020, Walton Smith wrote:
> >
> >
> > I?m having trouble with building AMBER. After I ./run_cmake in terminal,
> > the configuration never runs to completion. Here is the error log and
> > output log associated with my difficulties. Please let me know what I can
> > do to fix this issue, I would greatly appreciate it. Just to let you know,
> > I?m not very familiar with terminal so this is all pretty new to me.
>
> The most helpful file to post is "cmake.log", which is created when you
> use the "run_cmake" script. It also helps to give information about
> your operating system and environment. It looks like you are using OSX,
> but (a) which version? and (b) do you have any extra tools installed,
> such as homebrew or macports? Did you do anything unusual in
> installation, that is beyond what is suggested here?
>
> https://urldefense.com/v3/__https://ambermd.org/InstMacOS.php__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7DKbuj9uA$
>
> ...thanks...dac
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Mon, 27 Jul 2020 13:48:48 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Error building Amber
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20200727174848.zh4vutjc5fjkrpih.oq-fs-191g302-a.rad.rutgers.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> On Mon, Jul 27, 2020, Walton Smith wrote:
> >
> >
> > I?m having trouble with building AMBER. After I ./run_cmake in terminal,
> > the configuration never runs to completion. Here is the error log and
> > output log associated with my difficulties. Please let me know what I can
> > do to fix this issue, I would greatly appreciate it. Just to let you know,
> > I?m not very familiar with terminal so this is all pretty new to me.
>
> It's best to post the "cmake.log" file that is created by run_cmake.
>
> Also, let us know about your operating system and configuration. It
> looks like you are using OSX, but which version? and is there anything
> odd about your setup (is homebrew or something like that installed)?
> What do you have (if anything) in your /usr/local/lib folder?
>
> ...thanks....dac
>
>
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7ADQUNa8w$
>
>
> End of AMBER Digest, Vol 3076, Issue 1
> **************************************
    
    ------------------------------
    
    Message: 7
    Date: Tue, 28 Jul 2020 09:14:47 +0000
    From: Gustaf Olsson <gustaf.olsson.lnu.se>
    Subject: Re: [AMBER] Error building Amber
    To: AMBER Mailing List <amber.ambermd.org>
    Message-ID: <3bf80ac82f224472ae6db872faa1fda8.lnu.se>
    Content-Type: text/plain; charset="Windows-1252"
    
    Hello Walton
    
    
    I don't know what version of Xcode you are using though the 'ld: unknown option: --no-as-needed' seems to resemble a problem that has previously occurred.
    
    
    Ignoring this, from you logs I see that you are using gcc-8.2.0, if you check some previous posts I've made it seems that trying to compile amber under macOS using the gnu gcc compilers higher then version 7 will not work.
    
    
    Switching is not completely straightforward using homebrew as it will always opt for the most resent version of gcc.
    
    
    I have not yet double-checked though from what I remember, do a:
    
    
        $ brew install gcc.7
    
    
    and then
    
    
        $ CC=/usr/bin/clang && CXX=/usr/bin/clang++ && FC=/usr/local/bin/gfortran-7
    
    
    followed by a
    
    
        $ ./run_cmake MANUAL
    
    
    I would do this in a clean extracted build directory as I have seem complaints from cmake regarding residual files before.
    
    
    This should get you a serial version installed. Please let me know if this worked, otherwise I'll have to consult my notes later today. I have tried to get a working openMPI compilation as well though so far I have struck out completely.
    
    
    Best regards
    
    // Gustaf
    
    ________________________________
    Fr?n: Walton Smith <smit7450.mylaurier.ca>
    Skickat: den 27 juli 2020 21:50:54
    Till: AMBER Mailing List
    ?mne: Re: [AMBER] Error building Amber
    
    Hey Dac,
    
    I?m using Catalina (10.15.5), and I do have homebrew from when I installed the open source PyMOL. In my /usr/local/lib folder I have cmake, docker, python3.7 and python 3.8 along with an unknown pkgconfig folder and several lib?.dylib and .a files. I have attached the cmake.log file. Let me know if you might have any idea. Thank you so much for getting back to me so fast.
    
    
    WS
    
> On Jul 27, 2020, at 1:48 PM, David A Case <david.case.rutgers.edu> wrote:
>
> On Mon, Jul 27, 2020, Walton Smith wrote:
>>
>>
>> I?m having trouble with building AMBER. After I ./run_cmake in terminal,
>> the configuration never runs to completion. Here is the error log and
>> output log associated with my difficulties. Please let me know what I can
>> do to fix this issue, I would greatly appreciate it. Just to let you know,
>> I?m not very familiar with terminal so this is all pretty new to me.
>
> It's best to post the "cmake.log" file that is created by run_cmake.
>
> Also, let us know about your operating system and configuration. It
> looks like you are using OSX, but which version? and is there anything
> odd about your setup (is homebrew or something like that installed)?
> What do you have (if anything) in your /usr/local/lib folder?
>
> ...thanks....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7ADQUNa8w$
    
    _______________________________________________
    AMBER mailing list
    AMBER.ambermd.org
    https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7ADQUNa8w$
    
    
    ------------------------------
    
    Message: 8
    Date: Tue, 28 Jul 2020 09:43:52 -0400
    From: David A Case <david.case.rutgers.edu>
    Subject: Re: [AMBER] Error building Amber
    To: AMBER Mailing List <amber.ambermd.org>
    Cc: Jamie Smith <jsmith.crackofdawn.onmicrosoft.com>
    Message-ID: <20200728134352.xtz3aw2pbyp42xph.pop-os.localdomain>
    Content-Type: text/plain; charset=utf-8; format=flowed
    
    On Mon, Jul 27, 2020, Walton Smith wrote:
>
> I?m using Catalina (10.15.5), and I do have homebrew from when I installed
> the open source PyMOL. In my /usr/local/lib folder I have cmake, docker,?
> python3.7 and python 3.8 along with an unknown pkgconfig folder and
> several lib?.dylib and .a files. I have attached the cmake.log file. Let
> me know if you might have any idea. Thank you so much for getting back to
> me so fast.
    
    Thanks for the details. Here is the error message from the cmake.log file:
    
    CMake Error at cmake/LibraryUtils.cmake:75 (message):
       Could not determine whether
       "/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/lib/libbz2.tbd"
       is a static or shared library, it does not have a known suffix.
    Call Stack (most recent call first):
       cmake/LibraryTracking.cmake:40 (get_lib_type)
       cmake/LibraryTracking.cmake:196 (using_external_library)
       cmake/3rdPartyTools.cmake:956 (import_libraries)
       CMakeLists.txt:194 (include)
    
    All Mac's have *.tbd files in the indicated directory, but this is the first
    problem report we have seen.
    
    Do you have a libbz2.dylib file in /usr/lib? I would
    think that the external library searching routine should find that one first.
    
    cc-ing to Jaime for his thoughts. Jamie: if the library search finds an
    unknown suffix, why not just ignore it, rather than exiting with an error?
    
    Here is info on .tbd files:
    
       https://urldefense.com/v3/__https://stackoverflow.com/questions/31450690/why-xcode-7-shows-tbd-instead-of-dylib__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7AmIOyiVQ$
    
    One possible other thing to try: My guess is that you are using the
    homebrew installation of cmake, and that might make your machine different
    from mine. Can you try the suggestion here:
    
        https://urldefense.com/v3/__https://ambermd.org/InstMacOS.php__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7DKbuj9uA$
    
    and get (as instructed) /Applications/Cmake.app/Contents/bin first in your
    PATH? That will have you use the version of cmake from cmake.org.
    (This might solve the problem, but it seems to be a bit of a stretch.)
    
    ....dac
    
    
    
    
    ------------------------------
    
    Message: 9
    Date: Tue, 28 Jul 2020 13:51:23 +0000
    From: "Hantz, Eric R." <hantz.2.buckeyemail.osu.edu>
    Subject: [AMBER] ASMD equil4 not producing output files
    To: "amber.ambermd.org" <amber.ambermd.org>
    Message-ID: <64566ABC-DD99-414C-944B-91279841B81A.contoso.com>
    Content-Type: text/plain; charset="utf-8"
    
    Hello,
    
    I was able to work through the ASMD tutorial without any issues. Now I am attempting to apply the work through to my system of interest, N-terminal domain of cardiac troponin C in a solvent box. I am running into an issue performing the equilibration 4 step. Equilibrations 1-3 complete without any issues, however equil4 does not generate any output files (mdout, or anything else specified in the line). The logfile of the job indicates that the job starts and continues until it hits the allotted walltime, but nothing seems to be going on. Any help on the matter or guidance would be greatly appreciated! Please let me know if attaching any files would be useful.
    
    Thank you,
    
    
    [signature_579283338]
    
    Eric Hantz
    Biophysics Graduate Program
    Lindert Lab
    2120 Newman Wolfrom
    
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    ------------------------------
    
    Message: 10
    Date: Tue, 28 Jul 2020 09:59:16 -0400
    From: David A Case <david.case.rutgers.edu>
    Subject: Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN
            FAILURE..."
    To: AMBER Mailing List <amber.ambermd.org>
    Message-ID: <20200728135916.lrwetp35zzk65dy4.pop-os.localdomain>
    Content-Type: text/plain; charset=utf-8; format=flowed
    
    On Tue, Jul 28, 2020, ??? wrote:
    
>I process the box boundry using equil trajectory mdcrd file to generate
>a correspoding nc file due to a partition of water moleculare out of
>box after equilation, and then open the nc file in the vmd, and select
>parameters "save coordinate,fist 499, last 499, stride 1" and save as
>DLF-equil-499.pdb file as QM/MM inuptfile (but box is gone from here)
>when the runing box stop, and then a new prmtop and incrd were generated
>from DLF-equil-499.pdb, I presume this is the case where the issue
>occured, but I do not know how to fix the issue, please help me, thank
>you.
    
    oooh...just use cpptraj for all of this!
    
    First, if it is a problem that water molecules are "out of the box" use the
    autoimage action in cpptraj to pack things back in. Then you can save the
    file as a restart file, also in cpptraj. There should be no reason to need to
    recreate a prmtop file here: all you have done is change the coordinates of
    some atoms. I'm not sure what you mean by the phrase "QM/MM inputfile", or
    why you what a PDB-format file.
    
    If you (for whatever reason) get a PDB-format file as an intermediate, you
    will need to manually add back in the box parameters in the tleap step, after
    your loadPdb command. Type "help set" and look for box information.
    
    ....dac
    
    
    
    
    ------------------------------
    
    Message: 11
    Date: Tue, 28 Jul 2020 10:03:42 -0400
    From: Walton Smith <smit7450.mylaurier.ca>
    Subject: Re: [AMBER] Error building Amber
    To: david.case.rutgers.edu, AMBER Mailing List <amber.ambermd.org>
    Message-ID: <92514BE3-920B-4773-A0A2-A6C307AA7632.mylaurier.ca>
    Content-Type: text/plain; charset=utf-8
    
    Hey guys,
    
    I have a libbz2.1.0.tbd file but no libbz2.dylib file in /usr/lib. My version of Xcode is version 11.6, and cmake was downloaded as instructed off of cmake.org. /Applications/Cmake.app/contents/bin was placed in my PATH through the command shown on https://urldefense.com/v3/__https://ambermd.org/InstMacOS.php__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7DKbuj9uA$ <https://urldefense.com/v3/__https://ambermd.org/InstMacOS.php__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7DKbuj9uA$ >. I installed the gnu gcc compiler you suggested (version 7) and extracted it to a clean build folder and nothing seemed to change.
    
    Thanks for looking into this for me.
    
    Best,
    WS
> On Jul 28, 2020, at 9:43 AM, David A Case <david.case.rutgers.edu> wrote:
>
> On Mon, Jul 27, 2020, Walton Smith wrote:
>>
>> I?m using Catalina (10.15.5), and I do have homebrew from when I installed
>> the open source PyMOL. In my /usr/local/lib folder I have cmake, docker,
>> python3.7 and python 3.8 along with an unknown pkgconfig folder and
>> several lib?.dylib and .a files. I have attached the cmake.log file. Let
>> me know if you might have any idea. Thank you so much for getting back to
>> me so fast.
>
> Thanks for the details. Here is the error message from the cmake.log file:
>
> CMake Error at cmake/LibraryUtils.cmake:75 (message):
> Could not determine whether
> "/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/lib/libbz2.tbd"
> is a static or shared library, it does not have a known suffix.
> Call Stack (most recent call first):
> cmake/LibraryTracking.cmake:40 (get_lib_type)
> cmake/LibraryTracking.cmake:196 (using_external_library)
> cmake/3rdPartyTools.cmake:956 (import_libraries)
> CMakeLists.txt:194 (include)
>
> All Mac's have *.tbd files in the indicated directory, but this is the first
> problem report we have seen.
>
> Do you have a libbz2.dylib file in /usr/lib? I would
> think that the external library searching routine should find that one first.
>
> cc-ing to Jaime for his thoughts. Jamie: if the library search finds an
> unknown suffix, why not just ignore it, rather than exiting with an error?
>
> Here is info on .tbd files:
>
> https://urldefense.com/v3/__https://stackoverflow.com/questions/31450690/why-xcode-7-shows-tbd-instead-of-dylib__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7AmIOyiVQ$
>
> One possible other thing to try: My guess is that you are using the
> homebrew installation of cmake, and that might make your machine different
> from mine. Can you try the suggestion here:
>
> https://urldefense.com/v3/__https://ambermd.org/InstMacOS.php__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7DKbuj9uA$
>
> and get (as instructed) /Applications/Cmake.app/Contents/bin first in your
> PATH? That will have you use the version of cmake from cmake.org.
> (This might solve the problem, but it seems to be a bit of a stretch.)
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7ADQUNa8w$
    
    
    
    ------------------------------
    
    Message: 12
    Date: Tue, 28 Jul 2020 10:28:51 -0400
    From: Kenneth Huang <kennethneltharion.gmail.com>
    Subject: [AMBER] Tracking lifetime distance by closest of specific
            water IDs?
    To: AMBER Mailing List <amber.ambermd.org>
    Message-ID:
            <CALeh7kATwbXM6_T4aRuyxX8oAmbFt8rQLUF7JZb-hczEP47NSg.mail.gmail.com>
    Content-Type: text/plain; charset="UTF-8"
    
    Hi all,
    
    I have an odd scenerio where I'm trying to track the full distance lifetime
    of a subset of waters from an initial time point, ie frame 1, from a group
    of bases over 25 ns chunks of time. I'm having an issue in tracking all the
    waters though, in that if I use something like
    
    closest 17130 :8-10&!(.H=) noimage first closestout closest_s2_200
    outprefix closest_s2
    
    Where I have a total of 17131 waters in my box, but the problem I'm running
    into is that a number of those waters move so far away they're the
    furtherest water, so aren't recorded.
    
    I tried stripping out the all but the waters I'm interested in, but I ran
    into two issue where I couldn't tell if it was actually leaving the right
    waters, and my input for closest has it as N=total number of waters in the
    box.
    
    If it were just one residue, I'd try something with distance to get the
    missing distance like
    
    dist :WATID.O :8.CA out waterid_8ca.out
    
    And just take the min distance of the atoms in the group. But given there's
    three bases, the number of atoms to the water gets large. Given that, I
    feel like there's a simple solution that I'm just not thinking of?
    
    Best,
    
    Kenneth
    
    --
    Ask yourselves, all of you, what power would hell have if those imprisoned
    here could not dream of heaven?
    
    
    ------------------------------
    
    Message: 13
    Date: Tue, 28 Jul 2020 10:48:49 -0500
    From: Pinky Mazumder <pmazumder67.gmail.com>
    Subject: Re: [AMBER] Interaction of cellulose-hemicellulose
    To: AMBER Mailing List <amber.ambermd.org>
    Message-ID:
            <CAFoDHbgkLFdnGO+QPa0YSz4hMX8WnTrBs43c553NOEaL9rmXuA.mail.gmail.com>
    Content-Type: text/plain; charset="UTF-8"
    
    Hi Lachele,
    
    Still I am having problems with the methyl derivative. Could you please
    share the command of checking derivative charge on the molecule?
    
    Thanks!
    
    On Mon, Apr 20, 2020 at 1:48 AM Lachele Foley <lf.list.gmail.com> wrote:
    
> What do you mean by "converted"? Do you mean that you added TER cards
> to the PDB file? Did you do anything else?
>
> The way to really check bonding is to generate topology/coordinate
> files (parm7/rst7) and then load them into a viewer like VMD or
> Chimera. When I do that, and output a set of pamr7/rst7 files, the
> bonding looks ok. I don't have xleap at easy access at the moment, so
> I'm can't check the behavior there, but it's not super important.
>
> Note that you will also need to alter the charge on the C atom where
> the MEX is attached. The website does that automatically where it
> can, but there is no standard way to encode charge in a PDB file, so
> if you need to use the PDB file like you are, then you will need to
> adjust charge. The doc is below.
>
>
> https://urldefense.com/v3/__http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7ACK1W-Sg$
>
> I used these commands in tleap:
>
> source leaprc.GLYCAM_06j-1
> m = loadpdb hema_TER.pdb ## I added TER cards to the PDB file you
> sent a couple emails ago
> check m ## this gets tleap to perform some simple checks on your
> molecule, including total charge - should be zero if correct
> saveamberparm m m.parm7 m.rst7
> quit
>
> Then, I loaded them into vmd with:
>
> vmd m.parm7 m.rst7
>
> Make sure that this works by itself, then try to combine this and your
> other molecule.
>
> I've attached the PDB file with the TER cards added.
>
> Let me know if you have other questions.
>
> On Mon, Apr 20, 2020 at 1:05 AM Pinky Mazumder <pmazumder67.gmail.com>
> wrote:
> >
> > Hi Lachele,
> >
> > Hope you are doing well.
> >
> > I am facing another problem. I have build the hemicellulose chain using
> glycam carbo builder. so, for loading it in xleap, it needed to be
> converted.
> >
> >
> > The converted pdb looks fine in vmd. However, when I have loaded it into
> xleap, I found that the alpha-glucoronic residue have detached from the
> beta-xylose chains.
> >
> >
> > Attached is the image of vmd as well as xleap. Could you please tell me
> why this is happening?
> >
> >
> > Thank you.
> >
> > Sincerely,
> > pinky
> >
> > On Sat, Apr 18, 2020 at 2:21 AM Lachele Foley <lf.list.gmail.com> wrote:
> >>
> >> Sorry I didn't reply before now. Did you figure it out? Do you still
> >> need help?
> >>
> >> On Fri, Apr 17, 2020 at 5:28 PM Pinky Mazumder <pmazumder67.gmail.com>
> wrote:
> >> >
> >> > Hi Lachele,
> >> >
> >> > As you said about the combine command. It works.
> >> >
> >> > Thank you so much.
> >> >
> >> > Sincerely,
> >> > Pinky
> >> >
> >> > On Fri, Apr 17, 2020 at 9:59 AM Pinky Mazumder <pmazumder67.gmail.com>
> wrote:
> >> >>
> >> >> Also I do not have the Amber style pdb file. Do I need this for
> combining the two pdb?
> >> >>
> >> >> Thank you.
> >> >>
> >> >> Sincerely,
> >> >> Pinky
> >> >>
> >> >> On Fri, Apr 17, 2020 at 2:45 AM Pinky Mazumder <
> pmazumder67.gmail.com> wrote:
> >> >>>
> >> >>> Thank you for your cordial response.
> >> >>>
> >> >>> Here I have attached the two pdb files of cellulose and
> hemicellulose.
> >> >>>
> >> >>> I need to combine those chain as a single pdb so that I can run the
> relaxation.
> >> >>>
> >> >>>
> >> >>> Thank you again.
> >> >>>
> >> >>> Sincerely,
> >> >>> Pinky
> >> >>>
> >> >>> On Fri, Apr 17, 2020 at 1:06 AM Lachele Foley <lf.list.gmail.com>
> wrote:
> >> >>>>
> >> >>>> That usually means you have a bonding issue. You will often need
> to
> >> >>>> make little edits to your PDB file and/or leap commands to get
> carbs
> >> >>>> to be loaded properly.
> >> >>>>
> >> >>>> Did you download the amber-style pdb file? Can you send me your
> pdb file?
> >> >>>>
> >> >>>> On Fri, Apr 17, 2020 at 1:59 AM Pinky Mazumder <
> pmazumder67.gmail.com> wrote:
> >> >>>> >
> >> >>>> > Hi Lachele,
> >> >>>> >
> >> >>>> > Thank you for your reply.
> >> >>>> >
> >> >>>> >
> >> >>>> > I have build the hemicellulose using glycam carbohydrate builder
> and then I
> >> >>>> > am trying to load the pdb file of ''hemicellulose'' using
> loadpdb command
> >> >>>> > in xleap.
> >> >>>> >
> >> >>>> > But, It shows the error !FATAL: Message: Atom named C1 from
> 4LA did not
> >> >>>> > match !
> >> >>>> >
> >> >>>> > Attached is the screenshot.
> >> >>>> >
> >> >>>> > Do you have any idea why this is happening?
> >> >>>> >
> >> >>>> > Any help would be appreciated.
> >> >>>> >
> >> >>>> >
> >> >>>> > Thank you again.
> >> >>>> >
> >> >>>> >
> >> >>>> > Sincerely,
> >> >>>> > Pinky
> >> >>>> >
> >> >>>> > On Thu, Apr 16, 2020 at 3:23 AM Lachele Foley <lf.list.gmail.com>
> wrote:
> >> >>>> >
> >> >>>> > > I usually use tleap rather than xleap, but you should be able
> to use
> >> >>>> > > either. See my previous reply, but also consider the 'combine'
> >> >>>> > > command.
> >> >>>> > >
> >> >>>> > > Learning to use xleap or tleap takes a little time, but the
> Amber
> >> >>>> > > manual does a pretty good job of describing the functions.
> >> >>>> > >
> >> >>>> > > On Wed, Apr 15, 2020 at 11:14 PM Pinky Mazumder <
> pmazumder67.gmail.com>
> >> >>>> > > wrote:
> >> >>>> > > >
> >> >>>> > > > Dear Amber Users,
> >> >>>> > > >
> >> >>>> > > > I have built cellulose chain using xleap command. On the
> other hand,
> >> >>>> > > > I have made the chain of hemicellulose using GLYCAM_06
> carbohydrate
> >> >>>> > > builder.
> >> >>>> > > >
> >> >>>> > > > Now, I need to put the chain close together.
> >> >>>> > > >
> >> >>>> > > >
> >> >>>> > > > So, my question is, how can I make the both chains closer
> together?
> >> >>>> > > Should
> >> >>>> > > > I load the chain of hemicellulose in xleap? If it is, then
> what is the
> >> >>>> > > > command for this job?
> >> >>>> > > >
> >> >>>> > > >
> >> >>>> > > > Any help would be appreciated. Please forgive me if I am
> asking something
> >> >>>> > > > silly.
> >> >>>> > > >
> >> >>>> > > > Thank you.
> >> >>>> > > >
> >> >>>> > > > --
> >> >>>> > > > Pinky
> >> >>>> > > > AL,US
> >> >>>> > > > _______________________________________________
> >> >>>> > > > AMBER mailing list
> >> >>>> > > > AMBER.ambermd.org
> >> >>>> > > > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7ADQUNa8w$
> >> >>>> > >
> >> >>>> > >
> >> >>>> > >
> >> >>>> > > --
> >> >>>> > > :-) Lachele
> >> >>>> > > Lachele Foley
> >> >>>> > > CCRC/UGA
> >> >>>> > > Athens, GA USA
> >> >>>> > >
> >> >>>> > > _______________________________________________
> >> >>>> > > AMBER mailing list
> >> >>>> > > AMBER.ambermd.org
> >> >>>> > > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7ADQUNa8w$
> >> >>>> > >
> >> >>>> >
> >> >>>> >
> >> >>>> > --
> >> >>>> > Pinky
> >> >>>> > AL,US
> >> >>>> > _______________________________________________
> >> >>>> > AMBER mailing list
> >> >>>> > AMBER.ambermd.org
> >> >>>> > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7ADQUNa8w$
> >> >>>>
> >> >>>>
> >> >>>>
> >> >>>> --
> >> >>>> :-) Lachele
> >> >>>> Lachele Foley
> >> >>>> CCRC/UGA
> >> >>>> Athens, GA USA
> >> >>>>
> >> >>>> _______________________________________________
> >> >>>> AMBER mailing list
> >> >>>> AMBER.ambermd.org
> >> >>>> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7ADQUNa8w$
> >> >>>
> >> >>>
> >> >>>
> >> >>> --
> >> >>> Pinky
> >> >>> AL,US
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Pinky, Sharmi
> >> >> AL,US
> >> >
> >> >
> >> >
> >> > --
> >> > Pinky, Sharmi
> >> > AL,US
> >>
> >>
> >>
> >> --
> >> :-) Lachele
> >> Lachele Foley
> >> CCRC/UGA
> >> Athens, GA USA
> >
> >
> >
> > --
> > Pinky, Sharmi
> > AL,US
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7ADQUNa8w$
>
    
    
    --
    Pinky, Sharmi
    AL,US
    
    
    ------------------------------
    
    Message: 14
    Date: Tue, 28 Jul 2020 12:56:35 -0400
    From: Adrian Roitberg <roitberg.ufl.edu>
    Subject: Re: [AMBER] ASMD equil4 not producing output files
    To: <amber.ambermd.org>
    Message-ID: <17cb927a-766f-cdad-5f1a-160739531843.ufl.edu>
    Content-Type: text/plain; charset="utf-8"; format=flowed
    
    One possibility is that the output to the forces file is not being
    flushed, so if you finished your job due to walltime, that file is not
    really populated.
    
    To test: change nstlim to a much smaller number and see what happens if
    the job finishes on time.
    
    adrian
    
    
    On 7/28/20 9:51 AM, Hantz, Eric R. wrote:
> [External Email]
>
> Hello,
>
> I was able to work through the ASMD tutorial without any issues. Now I am attempting to apply the work through to my system of interest, N-terminal domain of cardiac troponin C in a solvent box. I am running into an issue performing the equilibration 4 step. Equilibrations 1-3 complete without any issues, however equil4 does not generate any output files (mdout, or anything else specified in the line). The logfile of the job indicates that the job starts and continues until it hits the allotted walltime, but nothing seems to be going on. Any help on the matter or guidance would be greatly appreciated! Please let me know if attaching any files would be useful.
>
> Thank you,
>
>
> [signature_579283338]
>
> Eric Hantz
> Biophysics Graduate Program
> Lindert Lab
> 2120 Newman Wolfrom
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=hzER9-l954M-54xBbIK46WeD-nxPQggq6NMnCb4xKR4&s=v_pZaFuBUPHczTNt2dcbx2BYwBOKahzd6kYLsyDJaIs&e=
    
    --
    Dr. Adrian E. Roitberg
    V.T. and Louise Jackson Professor in Chemistry
    Department of Chemistry
    University of Florida
    roitberg.ufl.edu
    352-392-6972
    
    
    
    ------------------------------
    
    Message: 15
    Date: Tue, 28 Jul 2020 17:05:00 +0000
    From: "Samuel A. Ratliff" <Samuel.Ratliff17.kzoo.edu>
    Subject: [AMBER] Issue heating system in equilibration step
    To: "amber.ambermd.org" <amber.ambermd.org>
    Message-ID: <1595955900987.99794.kzoo.edu>
    Content-Type: text/plain; charset="iso-8859-1"
    
    Hello all,
    
    
    I've been trying to equilibrate a protein embedded in a lipid bilayer and have been having some issues. So far, I've been roughly using the AMBER lipid tutorial at
    
    https://urldefense.com/v3/__http://ambermd.org/tutorials/advanced/tutorial16/index.html__;!!KGKeukY!lN14Oc3EAawXARkPiC0YkvcMFtNhgRtkY2S0_LDYPikDvqiXhEei700LO1hTmYxJt7DOyFE1Qg$ as a guide. I've been able to minimize the system in three phases, minimizing the waters, then the waters and the lipids, then minimizing the whole system. However, when I attempt to heat the system, pmemd.cuda dumps core with the following message:
    
    
    *** Error in `pmemd.cuda': double free or corruption (out): 0x000000000448df70 ***
    
    In the heat.out file where AMBER writes its output, the last line is "LOADING THE CONSTRAINED ATOMS AS GROUPS". AMBER also writes a NetCDF trajectory file, but when I view it in VMD, there are no atoms and the size of the NetCDF file is significantly smaller than I expect. I've opened the min_system.rst file that the heating step starts from in VMD and it seems to be fine. I've also been able to minimize the min_system.rst file again, so it doesn't seem like the restart file is the problem. From a conceptual standpoint, I was also unsure if when heating the system, I should restrain only the protein (resids 1-498) or the protein and the lipids (resids 1-1215). I've also tried removing the constraints on the system and it dumps core at the same place, though doesn't print "LOADING THE CONSTRAINED ATOMS AS GROUPS" and instead prints a line of dashes like the file was going to go on to the next section of the output.
    
    
    Below is my heat.out file. (Note: I know that AMBER16 is not particularly current, but my lab has custom code written for AMBER16 that necessitates its use.) Any suggestions to fix this issue or insights into what is going wrong are welcome. Thanks!
    
    
              -------------------------------------------------------
              Amber 16 PMEMD 2016
              -------------------------------------------------------
    
    | PMEMD implementation of SANDER, Release 16
    
    | Run on 07/28/2020 at 12:39:48
    
    | Executable path: pmemd.cuda
    | Working directory: /media/furgelab/Store/archive/sam_ratliff/simulations/lipid/1_lipid/2019.08.13_1/eq
    | Hostname: Unknown
      [-O]verwriting output
    
    File Assignments:
    | MDIN: /home/furgelab/scripts/MD/inputs//heat_lipid.in
    | MDOUT: heat/heat.out
    | INPCRD: minimization/min_system.rst
    | PARM: ../build/system/1_lipid.prmtop
    | RESTRT: heat/heat.rst
    | REFC: minimization/min_system.rst
    | MDVEL: mdvel
    | MDEN: mden
    | MDCRD: heat/heat.nc
    | MDINFO: heat/heat.mdinfo
    | MDFRC: mdfrc
    
    
     Here is the input file:
    
    Heating up the system equilibration stage 1
     &cntrl
      imin=0, irest=0,
      ntx=1, ig=-1,
      nstlim=25000,
      dt=0.002,
      ntpr=7, ntwr=7, ntwx=7,
      tempi=0.0, temp0=310.0,
      ntt=3, gamma_ln=5, ntb=1, ntp=0,
      ntc=2, ntf=2, nmropt = 1,
      cut=9, ntr=1,
      restraintmask='(:1-498.CA,C,N)', !was :1-1215
      restraint_wt=4.0,
      ioutfm=1,
      iwrap=1,
     &end
     &wt TYPE='TEMP0', istep1=0, istep2=125000,
      value1=0.0, value2=310.0, /
     &wt TYPE='END' /
    
    
    Note: ig = -1. Setting random seed to 78217 based on wallclock time in
          microseconds.
    
    |--------------------- INFORMATION ----------------------
    | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
    | Version 16.0.0
    |
    | 02/25/2016
    |
    | Implementation by:
    | Ross C. Walker (SDSC)
    | Scott Le Grand (nVIDIA)
    |
    | Precision model in use:
    | [SPFP] - Single Precision Forces, 64-bit Fixed Point
    | Accumulation. (Default)
    |
    |--------------------------------------------------------
    
    |----------------- CITATION INFORMATION -----------------
    |
    | When publishing work that utilized the CUDA version
    | of AMBER, please cite the following in addition to
    | the regular AMBER citations:
    |
    | - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
    | Poole; Scott Le Grand; Ross C. Walker "Routine
    | microsecond molecular dynamics simulations with
    | AMBER - Part II: Particle Mesh Ewald", J. Chem.
    | Theory Comput., 2013, 9 (9), pp3878-3888,
    | DOI: 10.1021/ct400314y.
    |
    | - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
    | Duncan Poole; Scott Le Grand; Ross C. Walker
    | "Routine microsecond molecular dynamics simulations
    | with AMBER - Part I: Generalized Born", J. Chem.
    | Theory Comput., 2012, 8 (5), pp1542-1555.
    |
    | - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
    | "SPFP: Speed without compromise - a mixed precision
    | model for GPU accelerated molecular dynamics
    | simulations.", Comp. Phys. Comm., 2013, 184
    | pp374-380, DOI: 10.1016/j.cpc.2012.09.022
    |
    |--------------------------------------------------------
    
    |------------------- GPU DEVICE INFO --------------------
    |
    | CUDA_VISIBLE_DEVICES: not set
    | CUDA Capable Devices Detected: 3
    | CUDA Device ID in use: 0
    | CUDA Device Name: GeForce GTX 980 Ti
    | CUDA Device Global Mem Size: 6078 MB
    | CUDA Device Num Multiprocessors: 22
    | CUDA Device Core Freq: 1.29 GHz
    |
    |--------------------------------------------------------
    
    
    | Conditional Compilation Defines Used:
    | PUBFFT
    | BINTRAJ
    | CUDA
    | EMIL
    
    | Largest sphere to fit in unit cell has radius = 53.247
    
    | New format PARM file being parsed.
    | Version = 1.000 Date = 08/13/19 Time = 12:46:28
    
    | Note: 1-4 EEL scale factors are being read from the topology file.
    
    | Note: 1-4 VDW scale factors are being read from the topology file.
    | Duplicated 0 dihedrals
    
    | Duplicated 0 dihedrals
    
    --------------------------------------------------------------------------------
       1. RESOURCE USE:
    --------------------------------------------------------------------------------
    
     getting box info from netcdf restart file
     NATOM = 69270 NTYPES = 32 NBONH = 52859 MBONA = 16283
     NTHETH = 56126 MTHETA = 19684 NPHIH = 94026 MPHIA = 61862
     NHPARM = 0 NPARM = 0 NNB = 261952 NRES = 10976
     NBONA = 16283 NTHETA = 19684 NPHIA = 61862 NUMBND = 106
     NUMANG = 233 NPTRA = 258 NATYP = 63 NPHB = 1
     IFBOX = 1 NMXRS = 73 IFCAP = 0 NEXTRA = 0
     NCOPY = 0
    
    | Coordinate Index Table dimensions: 21 24 26
    | Direct force subcell size = 5.0711 5.0986 5.1183
    
         BOX TYPE: RECTILINEAR
    
    --------------------------------------------------------------------------------
       2. CONTROL DATA FOR THE RUN
    --------------------------------------------------------------------------------
    
    default_name
    
    General flags:
         imin = 0, nmropt = 1
    
    Nature and format of input:
         ntx = 1, irest = 0, ntrx = 1
    
    Nature and format of output:
         ntxo = 2, ntpr = 7, ntrx = 1, ntwr = 7
         iwrap = 1, ntwx = 7, ntwv = 0, ntwe = 0
         ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0
    
    Potential function:
         ntf = 2, ntb = 1, igb = 0, nsnb = 25
         ipol = 0, gbsa = 0, iesp = 0
         dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
    
    Frozen or restrained atoms:
         ibelly = 0, ntr = 1
         restraint_wt = 4.00000
    
    Molecular dynamics:
         nstlim = 25000, nscm = 0, nrespa = 1
         t = 0.00000, dt = 0.00200, vlimit = -1.00000
    
    Langevin dynamics temperature regulation:
         ig = 78217
         temp0 = 310.00000, tempi = 0.00000, gamma_ln= 5.00000
    
    SHAKE:
         ntc = 2, jfastw = 0
         tol = 0.00001
    
    NMR refinement options:
         iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1
         scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
    
    | Intermolecular bonds treatment:
    | no_intermolecular_bonds = 1
    
    | Energy averages sample interval:
    | ene_avg_sampling = 7
    
    Ewald parameters:
         verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
         vdwmeth = 1, eedmeth = 1, netfrc = 1
         Box X = 106.494 Box Y = 122.367 Box Z = 133.077
         Alpha = 90.000 Beta = 90.000 Gamma = 90.000
         NFFT1 = 108 NFFT2 = 128 NFFT3 = 128
         Cutoff= 9.000 Tol =0.100E-04
         Ewald Coefficient = 0.30768
         Interpolation order = 4
    
        LOADING THE CONSTRAINED ATOMS AS GROUPS
    
    
    Thanks,
    
    Sam Ratliff
    
    
    ------------------------------
    
    Message: 16
    Date: Tue, 28 Jul 2020 10:55:43 -0700
    From: Lod King <lodking407.gmail.com>
    Subject: [AMBER] AMD parameter: protein residue should count ligand or
            not
    To: AMBER Mailing List <amber.ambermd.org>
    Message-ID:
            <CAFVhGCTrskaOYT1-R0sbRHEWwUPANzO6cy+Rbponh4QPguMGaA.mail.gmail.com>
    Content-Type: text/plain; charset="UTF-8"
    
    Hi, amber
    
    I am setting parameters to run AMD.
    
    Should I count the ligand to the 'protein residue" flag in amd input file
    or only the total number of protein residues?
    
    Amber manual 18
    section 20.2.3 example:
    
    Average Dihedral : 611.5376 (based on MD simulations)
    Average EPtot : -53155.3104 (based on MD simulations)
    total ATOMS=16950
    *protein residues=64*
    
    
    ------------------------------
    
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    End of AMBER Digest, Vol 3077, Issue 1
    **************************************
    

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Received on Wed Jul 29 2020 - 13:30:02 PDT
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