*Correction. I was able to run Run.pymsmt. Please disregard the following
error message.
./Run.pymsmt: line 12: mcpbpy.out: Permission denied
./Run.pymsmt: Program error
On Thu, Jul 9, 2015 at 2:16 PM, Eleftherios A P Lambros <tlambros.uci.edu>
wrote:
> Hello,
>
> I tried using
>
> python -c 'import numpy'
>
> but that yielded,
>
> Traceback (most recent call last):
> File "<string>", line 1, in <module>
> ImportError: No module named numpy
>
> Running Run.pymsmt in $AMBERHOME/AmberTools/test/pymsmt/mcpb yields
>
> ./Run.pymsmt: line 12: mcpbpy.out: Permission denied
> ./Run.pymsmt: Program error
>
> with a mcpbpy.out file of
>
> Traceback (most recent call last):
> File "../../../bin/MCPB.py", line 46, in <module>
> from mcpb.gene_model_files import get_ms_resnames, gene_model_files
> File
> "/home/rayl/amber15-with-patches/lib/python2.6/site-packages/mcpb/gene_model_files.py",
> line 8, in <module>
> from pymsmtmol.cal import calc_bond
> File
> "/home/rayl/amber15-with-patches/lib/python2.6/site-packages/pymsmtmol/cal.py",
> line 5, in <module>
> import numpy
> ImportError: No module named numpy
>
> Thanks for any help. *Note that I am sourced to amber.sh*
>
> Regards,
> Eleftherios (Teri) Lambros
>
>
> On Wed, Jul 8, 2015 at 12:00 PM, <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: About python usage in AmberTools (Eiros Zamora, Juan)
>> 2. Re: About python usage in AmberTools (Jason Swails)
>> 3. Re: About python usage in AmberTools (Hai Nguyen)
>> 4. NumPy Import Error for MCPB.py on Amber15
>> (Eleftherios A P Lambros)
>> 5. Re: NumPy Import Error for MCPB.py on Amber15 (Takeshi Baba)
>> 6. Re: NumPy Import Error for MCPB.py on Amber15 (Hai Nguyen)
>> 7. issue using CUDA+MPI+OpenMP (?ric Germaneau)
>> 8. Re: issue using CUDA+MPI+OpenMP (Gerald Monard)
>> 9. Paramentrization of a Uracil base with an O3' terminus
>> deprotonated. (giulia palermo)
>> 10. help in amber (Robin Jain)
>> 11. Re: Paramentrization of a Uracil base with an O3' terminus
>> deprotonated. (Jason Swails)
>> 12. Re: help in amber (Jason Swails)
>> 13. Re: About python usage in AmberTools (Juan Eiros Zamora)
>> 14. Re: About python usage in AmberTools (Jason Swails)
>> 15. Re: About python usage in AmberTools (Juan Eiros Zamora)
>> 16. Re: About python usage in AmberTools (Jason Swails)
>> 17. Re: Paramentrization of a Uracil base with an O3' terminus
>> deprotonated. (giulia palermo)
>> 18. Re: About python usage in AmberTools (Juan Eiros Zamora)
>> 19. Re: About python usage in AmberTools (Hai Nguyen)
>> 20. Re: About python usage in AmberTools (Hai Nguyen)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 7 Jul 2015 19:50:45 +0000
>> From: "Eiros Zamora, Juan" <j.eiros-zamora14.imperial.ac.uk>
>> Subject: Re: [AMBER] About python usage in AmberTools
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <E7799EECCDE21F40A8F022CD1509322A35CD0110.icexch-m3.ic.ac.uk>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi Jason,
>>
>> So once I've created the environment py27 with conda, how do I use it
>> with Amber?
>>
>> I don't have access to my workstation right now, but should it be
>> something like
>>
>> ./configure --with-python py27
>> make install
>>
>> I prefer to do that rather than forcing it to use Python 3, as I would
>> like to make full use of the AmberTools programs.
>>
>> Thanks for the info,
>>
>> Juan
>> ________________________________________
>> De: Jason Swails [jason.swails.gmail.com]
>> Enviado: martes, 07 de julio de 2015 19:55
>> Para: AMBER Mailing List
>> Asunto: Re: [AMBER] About python usage in AmberTools
>>
>> On Tue, Jul 7, 2015 at 2:05 PM, Juan Eiros Zamora <
>> j.eiros-zamora14.imperial.ac.uk> wrote:
>>
>> > Hi Amber users,
>> >
>> > I've recently downloaded AmberTools15 and followed all the installation
>> > steps succesfully on a RHEL6. But when I try to do
>> >
>> > make test
>> >
>> > I get the following errors http://lpaste.net/42814355720372224 (copied
>> > in this link)
>> >
>> > The python version that I currently use is 3.4.3 installed with Anaconda
>> > 2.1.0 (64-bit) distribution. Also my PYTHONPATH is set to
>> >
>> >
>> /usr/local/amber15/lib/python2.7/site-packages:/usr/local/amber/lib/python2.7/site-packages
>> > after I source the $AMBERHOME/amber.sh script.
>> >
>> > So what's the python that AmberTools is trying to use? And how do I
>> > manage to add python packages to the AmberTools installation?
>> >
>>
>> Most of Amber's Python tools are written for Python 2. Some of them are
>> Python-3 compatible (I know ParmEd can be installed with Python 3, and I
>> *think* MMPBSA.py will work as well), but others are probably not.
>>
>> So the configure script looks for python2.7, python2.6, python2.5,
>> python2.4, and falls back to python if none of the previous choices are
>> available. You can always use conda to set up a new Python 2.7 virtual
>> environment:
>>
>> conda create -n py27 python=2.7
>>
>> And use that environment with Amber.
>>
>> If you want to force AmberTools to use your anaconda Python 3, you can use
>> "--with-python `which python`" when you run configure.
>>
>>
>> > I've previously experienced problems with other AmberTools
>> > programs, such as xparmed.py, or mdout_analyzer.py, (see errors here
>> > http://lpaste.net/7336825506265825280 ) in which python modules are
>> > missing; and I don't know how to add them because if I just do conda
>> > install package it will install it in my regular python distribution
>> > (although that the _tkinter that's missing I can't even find it using
>> > conda).
>> >
>>
>> ?conda should come with Tkinter already installed.
>> ?
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 7 Jul 2015 15:54:19 -0400
>> From: Jason Swails <jason.swails.gmail.com>
>> Subject: Re: [AMBER] About python usage in AmberTools
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <
>> CAEk9e3oOFJBBqBHohXAEMT6Hj2NHRbZF5tr4ZAQX83PVLh8jWQ.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> On Tue, Jul 7, 2015 at 3:50 PM, Eiros Zamora, Juan <
>> j.eiros-zamora14.imperial.ac.uk> wrote:
>>
>> > Hi Jason,
>> >
>> > So once I've created the environment py27 with conda, how do I use it
>> with
>> > Amber?
>> >
>>
>> ?You need to activate that environment:
>>
>> source activate py27
>>
>> Then AmberTools' configure should pick up that Python (as long as that's
>> the python that is run when you just type "python" in the terminal).
>> configure should output the Python that it finds and decides to use.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Tue, 7 Jul 2015 17:54:30 -0400
>> From: Hai Nguyen <nhai.qn.gmail.com>
>> Subject: Re: [AMBER] About python usage in AmberTools
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAFNMPM_fvKK58vtz7v+88ix7g1EJwhYUL8aTcH+fjmCPnQ=
>> D6w.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> .Juan:
>>
>> I myself get similar error with `conda` install. So the best solution for
>> now is install from github
>>
>>
>>
>> *git clone https://github.com/pytraj/pytraj
>> <https://github.com/pytraj/pytraj>cd pytrajpython ./setup.py install*
>>
>> Let me know if there is any problem. thanks.
>>
>> Hai
>>
>>
>> On Tue, Jul 7, 2015 at 2:33 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>>
>> > Hi,
>> >
>> > I can answer question about `pytraj`.
>> >
>> > This error "undefined symbol: _ZN14MaskTokenArray13SelectedChar_E"
>> likely
>> > indicates that you have old `libcpptraj.so` file somewhere.
>> >
>> > Since `pytraj` is in dev-status, it catch up with `cpptraj-dev` version
>> > and not work with version in official AT15.
>> >
>> > Can you try running this script from here:
>> > https://github.com/pytraj/pytraj/blob/master/scripts/find_libcpptraj.py
>> > `python find_libcpptraj.py`
>> >
>> > and let us know the output.
>> >
>> > Alternative, you can install from github (the most updated version).
>> >
>> >
>> >
>> > *git clone https://github.com/pytraj/pytraj
>> > <https://github.com/pytraj/pytraj>cd pytrajpython ./setup.py install*
>> >
>> > (`pytraj` will install `cpptraj-dev` from github for you. Make sure to
>> > read the instruction after the install finish)
>> >
>> > Hai
>> >
>> >
>> > On Tue, Jul 7, 2015 at 2:05 PM, Juan Eiros Zamora <
>> > j.eiros-zamora14.imperial.ac.uk> wrote:
>> >
>> >> Hi Amber users,
>> >>
>> >> I've recently downloaded AmberTools15 and followed all the installation
>> >> steps succesfully on a RHEL6. But when I try to do
>> >>
>> >> make test
>> >>
>> >> I get the following errors http://lpaste.net/42814355720372224 (copied
>> >> in this link)
>> >>
>> >> The python version that I currently use is 3.4.3 installed with
>> Anaconda
>> >> 2.1.0 (64-bit) distribution. Also my PYTHONPATH is set to
>> >>
>> >>
>> /usr/local/amber15/lib/python2.7/site-packages:/usr/local/amber/lib/python2.7/site-packages
>> >> after I source the $AMBERHOME/amber.sh script.
>> >>
>> >> So what's the python that AmberTools is trying to use? And how do I
>> >> manage to add python packages to the AmberTools installation?
>> >>
>> >> I've previously experienced problems with other AmberTools
>> >> programs, such as xparmed.py, or mdout_analyzer.py, (see errors here
>> >> http://lpaste.net/7336825506265825280 ) in which python modules are
>> >> missing; and I don't know how to add them because if I just do conda
>> >> install package it will install it in my regular python distribution
>> >> (although that the _tkinter that's missing I can't even find it using
>> >> conda).
>> >>
>> >> I've a second question also related to python. I've tried to install
>> the
>> >> pytraj program on my conda distribution like the Amber Manual suggests:
>> >> conda install --force -c pytraj pytraj-dev
>> >>
>> >> And it installs it correctly in my anaconda3 folder. Now if I open the
>> >> python interpreter and import pytraj, I get the following error
>> >> http://lpaste.net/3868115149562839040 . I don't know if this might be
>> >> related to the problems I've reported before? Or it could be an issue
>> >> related to the Cython code that's in pytraj? Just a guess based on my
>> >> little experience with python.
>> >>
>> >> I'm pretty stuck on this so any guidance on this matter would be
>> >> appreciated,
>> >>
>> >> Juan Eiros
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> >
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Tue, 7 Jul 2015 16:23:54 -0700
>> From: Eleftherios A P Lambros <tlambros.uci.edu>
>> Subject: [AMBER] NumPy Import Error for MCPB.py on Amber15
>> To: amber.ambermd.org
>> Message-ID:
>> <
>> CAE+dMzwO9KSaXbozcdVY1fFdR7Ays09_Oqe_4xkCq8Xvf-0W5g.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Hello,
>>
>> I am attempting to run MCPB.py but it cannot find the numpy module. This
>> is
>> on a Rocks cluster running CentOS with Python version 2.6.6. We have numpy
>> installed on the cluster, but it doesn?t seem to be able to find it. Here
>> is the input command and error message..
>>
>> $ MCPB.py -i TS3.in -s 1a
>>
>> Traceback (most recent call last):
>> File "/home/rayl/amber15-with-patches/bin/MCPB.py", line 46, in <module>
>> from mcpb.gene_model_files import get_ms_resnames, gene_model_files
>> File
>>
>> "/home/rayl/amber15-with-patches/lib/python2.6/site-packages/mcpb/gene_model_files.py",
>> line 8, in <module>
>> from pymsmtmol.cal import calc_bond
>> File
>>
>> "/home/rayl/amber15-with-patches/lib/python2.6/site-packages/pymsmtmol/cal.py",
>> line 5, in <module>
>> import numpy
>> ImportError: No module named numpy
>>
>> Any help is appreciated.
>>
>> Regards,
>> Eleftherios (Teri) Lambros
>> --
>> Mathematics, School of Physical Sciences
>> Biological Sciences, School of Biological Sciences
>> University of California: Irvine
>>
>> President, Anteaters Mathematics Club
>> Advocacy Committee, Biological Sciences Student Council
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Wed, 8 Jul 2015 08:39:25 +0900
>> From: Takeshi Baba <tbaba.cheng.es.osaka-u.ac.jp>
>> Subject: Re: [AMBER] NumPy Import Error for MCPB.py on Amber15
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <72D0BB8F-8746-49A5-A618-4787FBD4DEC2.cheng.es.osaka-u.ac.jp>
>> Content-Type: text/plain; charset=us-ascii
>>
>> Dear Eleftherios,
>>
>> Hi, I have a comment.
>>
>> To check the problem, please carry out Run.pymsmt in
>> $AMBERHOME/AmberTool/test/pymsmt/mcpb
>> If this problem works correctly, I think your input files for MCPB.py are
>> wrong.
>>
>> My system works correctly using MCPB.py.
>>
>> Best regards
>> Takeshi Baba
>>
>> --------------------------------------------------------------------------------------------------------
>> Takeshi Baba
>> Division of Chemical Engineering,
>> Department of Materials Engineering Science,
>> Graduate School of Engineering Science,
>> Osaka University, Toyonaka, Osaka 560-8531, JAPAN
>> Tel: +81-6-6850-6266, Fax: +81-6-6850-6268
>> e-mail: tbaba.cheng.es.osaka-u.ac.jp
>>
>> --------------------------------------------------------------------------------------------------------
>>
>>
>>
>>
>>
>>
>>
>> On 2015/07/08, at 8:23, Eleftherios A P Lambros <tlambros.uci.edu> wrote:
>>
>> > Eleftherios
>>
>>
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Tue, 7 Jul 2015 20:10:57 -0400
>> From: Hai Nguyen <nhai.qn.gmail.com>
>> Subject: Re: [AMBER] NumPy Import Error for MCPB.py on Amber15
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <
>> CAFNMPM9A5dFF+PGZCfKbVxQvyAdeEajRyTmrq-hcJtEgfx91bQ.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> can you try this command: python -c 'import numpy'
>>
>> if this does not work, you likely need to add numpy dir to PYTHONPATH.
>>
>> (Jason or others might have better solution).
>>
>> Hai
>> On Tue, Jul 7, 2015 at 7:23 PM, Eleftherios A P Lambros <tlambros.uci.edu
>> >
>> wrote:
>>
>> > Hello,
>> >
>> > I am attempting to run MCPB.py but it cannot find the numpy module.
>> This is
>> > on a Rocks cluster running CentOS with Python version 2.6.6. We have
>> numpy
>> > installed on the cluster, but it doesn?t seem to be able to find it.
>> Here
>> > is the input command and error message..
>> >
>> > $ MCPB.py -i TS3.in -s 1a
>> >
>> > Traceback (most recent call last):
>> > File "/home/rayl/amber15-with-patches/bin/MCPB.py", line 46, in
>> <module>
>> > from mcpb.gene_model_files import get_ms_resnames, gene_model_files
>> > File
>> >
>> >
>> "/home/rayl/amber15-with-patches/lib/python2.6/site-packages/mcpb/gene_model_files.py",
>> > line 8, in <module>
>> > from pymsmtmol.cal import calc_bond
>> > File
>> >
>> >
>> "/home/rayl/amber15-with-patches/lib/python2.6/site-packages/pymsmtmol/cal.py",
>> > line 5, in <module>
>> > import numpy
>> > ImportError: No module named numpy
>> >
>> > Any help is appreciated.
>> >
>> > Regards,
>> > Eleftherios (Teri) Lambros
>> > --
>> > Mathematics, School of Physical Sciences
>> > Biological Sciences, School of Biological Sciences
>> > University of California: Irvine
>> >
>> > President, Anteaters Mathematics Club
>> > Advocacy Committee, Biological Sciences Student Council
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> ------------------------------
>>
>> Message: 7
>> Date: Wed, 08 Jul 2015 14:12:45 +0800
>> From: ?ric Germaneau <germaneau.sjtu.edu.cn>
>> Subject: [AMBER] issue using CUDA+MPI+OpenMP
>> To: amber.ambermd.org
>> Message-ID: <559CBF5D.3040005.sjtu.edu.cn>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>> Dear all,
>>
>> I'm helping a user running Amber on our machine.
>> I basically compiled it doing
>>
>> ./configure -intelmpi -mkl -cuda -openmp intel
>>
>> We have two 8-cores CPU and two GPU per node, we use LSF as job scheduler.
>> I submit a 2 MPI process per node job.
>> Each of the process takes care of one GPU as expected, however only one
>> threads per MPI process is used (even if I set OMP_NUM_THREADS).
>> Is there a way to perform a multi-threading job using MPI and CUDA?
>> Thank you,
>>
>> ?ric.
>>
>> --
>> ?ric Germaneau (???), Specialist
>> Center for High Performance Computing
>> Shanghai Jiao Tong University
>> Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China
>> Email:germaneau.sjtu.edu.cn Mobi:+86-136-4161-6480 http://hpc.sjtu.edu.cn
>>
>>
>> ------------------------------
>>
>> Message: 8
>> Date: Wed, 08 Jul 2015 10:10:42 +0200
>> From: Gerald Monard <Gerald.Monard.univ-lorraine.fr>
>> Subject: Re: [AMBER] issue using CUDA+MPI+OpenMP
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <559CDB02.4070900.univ-lorraine.fr>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>> Hi,
>>
>> On 07/08/2015 08:12 AM, ?ric Germaneau wrote:
>> > Dear all,
>> >
>> > I'm helping a user running Amber on our machine.
>> > I basically compiled it doing
>> >
>> > ./configure -intelmpi -mkl -cuda -openmp intel
>>
>> As far as I known, the -openmp configuration option does not have any
>> effect on the compilation of pmemd (except for MIC?).
>>
>> >
>> > We have two 8-cores CPU and two GPU per node, we use LSF as job
>> scheduler.
>> > I submit a 2 MPI process per node job.
>> > Each of the process takes care of one GPU as expected, however only one
>> > threads per MPI process is used (even if I set OMP_NUM_THREADS).
>> > Is there a way to perform a multi-threading job using MPI and CUDA?
>>
>> The way pmemd.cuda works is that it uses 1 thread per GPU. Most of the
>> computations are done in the GPU (unlike NAMD for example), thus
>> multi-threading on the CPU is useless here.
>>
>> Gerald.
>>
>> > Thank you,
>> >
>> > ?ric.
>> >
>>
>> --
>>
>> ____________________________________________________________________________
>>
>> Prof. Gerald MONARD
>> SRSMC, Universit? de Lorraine, CNRS
>> Boulevard des Aiguillettes B.P. 70239
>> F-54506 Vandoeuvre-les-Nancy, FRANCE
>>
>> e-mail : Gerald.Monard.univ-lorraine.fr
>> tel. : +33 (0)383.684.381
>> fax : +33 (0)383.684.371
>> web : http://www.monard.info
>>
>>
>> ____________________________________________________________________________
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 9
>> Date: Wed, 8 Jul 2015 10:14:39 +0200
>> From: giulia palermo <giulia.palermo83.gmail.com>
>> Subject: [AMBER] Paramentrization of a Uracil base with an O3'
>> terminus deprotonated.
>> To: AMBER Mailing List <amber.ambermd.org>, Lorenzo Casalino
>> <lcasalino.sissa.it>
>> Message-ID:
>> <
>> CAHde_OY7-MdHJtTxAWAxDApML7aBiszZ-2PeME-tF-NNmCPcqA.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear all,
>>
>> we am parametrizing a Uracil base with an O3' terminus deprotonated.
>>
>> As specified by the AMBER tutorial and done by Cornell et al. JACS 117,
>> 1195, during the derivation of the Electrostatic Potential via QM
>> calculations, a methyl group is used for the capping of the O5', while the
>> O3' is capped with an hydrogen atom.
>> Subsequently, during the RESP fitting procedure, the TOTAL charge of the
>> capping metyl (.O5') and of the hydrogen (.O3') is set to ZERO.
>>
>> In our case, this can not be done, because the O3' terminus should be
>> deprotonated.
>> How do you suggest to proceed in such a way?
>>
>> Thank you very much
>> Giulia and Lorenzo
>>
>>
>> ------------------------------
>>
>> Message: 10
>> Date: Wed, 8 Jul 2015 15:01:26 +0530
>> From: Robin Jain <robinjain.chem.gmail.com>
>> Subject: [AMBER] help in amber
>> To: amber <amber.ambermd.org>
>> Message-ID:
>> <CA+QHj+mN+wFtFQgyRhFAtUkonGP=
>> y7DC1ef26VLQgpN67_k0KA.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear all,
>> i have simulate a organic molecule in 128 methanol in a cubic box of 21
>> angstrom and after 60ns production , i want to use final coordinate for
>> abinitio md, Therefore i load my trajectory in VMD to save last frame
>> coordinates but after loading i saw that all the methanol molecules are
>> too
>> much far away from each other and their coordinates are out of box, for
>> this i used another option given in Amber program such as ambpdb to save
>> coordinates but it also show to much variable coordinates , specially in
>> negative values. What is going wrong, Please help me in this regard.
>>
>> Thanking You.
>>
>> --
>> Robin Jain
>>
>>
>> ------------------------------
>>
>> Message: 11
>> Date: Wed, 8 Jul 2015 09:11:02 -0400
>> From: Jason Swails <jason.swails.gmail.com>
>> Subject: Re: [AMBER] Paramentrization of a Uracil base with an O3'
>> terminus deprotonated.
>> To: AMBER Mailing List <amber.ambermd.org>
>> Cc: Lorenzo Casalino <lcasalino.sissa.it>
>> Message-ID:
>> <
>> CAEk9e3qh+nFirj7v87tH7D0YoOKku5Dppnvp12skQg8uT88ggQ.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> On Wed, Jul 8, 2015 at 4:14 AM, giulia palermo <
>> giulia.palermo83.gmail.com>
>> wrote:
>>
>> > Dear all,
>> >
>> > we am parametrizing a Uracil base with an O3' terminus deprotonated.
>> >
>> > As specified by the AMBER tutorial and done by Cornell et al. JACS 117,
>> > 1195, during the derivation of the Electrostatic Potential via QM
>> > calculations, a methyl group is used for the capping of the O5', while
>> the
>> > O3' is capped with an hydrogen atom.
>> > Subsequently, during the RESP fitting procedure, the TOTAL charge of the
>> > capping metyl (.O5') and of the hydrogen (.O3') is set to ZERO.
>> >
>> > In our case, this can not be done, because the O3' terminus should be
>> > deprotonated.
>> > How do you suggest to proceed in such a way?
>> >
>>
>> ?The basic approach is to use capping groups to make sure you actually run
>> a QM calculation on a full molecule (not one with missing atoms and
>> dangling bonds -- that makes no sense in a QM calculation). However, you
>> never want the capping group to "steal" charge from the assigned partial
>> atomic charges of the fragment (since then you will wind up with a
>> non-integer charge). So when fitting charges, you apply the constraint
>> that the added fragments must carry a net neutral charge. This will make
>> sure that the fragment has the full charge you want.
>>
>> It's not entirely clear why you say "this cannot be done because the O3'
>> terminus should be deprotonated". The net charge of all atoms you add to
>> your fragment should be constrained to zero. If you are simulating a
>> deprotonated 3' terminus, then your net charge on the QM region should be
>> -2, but the constraint on the added methyl group (and any other added
>> atom)
>> should still be 0.
>>
>> Or maybe I didn't understand your question/problem?
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> ------------------------------
>>
>> Message: 12
>> Date: Wed, 8 Jul 2015 09:13:46 -0400
>> From: Jason Swails <jason.swails.gmail.com>
>> Subject: Re: [AMBER] help in amber
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <
>> CAEk9e3r0DP4pmk_FbMuY+0zNbyVT5mMWMwsq9zLiVvHSKXcuwQ.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> On Wed, Jul 8, 2015 at 5:31 AM, Robin Jain <robinjain.chem.gmail.com>
>> wrote:
>>
>> > Dear all,
>> > i have simulate a organic molecule in 128 methanol in a cubic box of 21
>> > angstrom and after 60ns production , i want to use final coordinate for
>> > abinitio md, Therefore i load my trajectory in VMD to save last frame
>> > coordinates but after loading i saw that all the methanol molecules are
>> too
>> > much far away from each other and their coordinates are out of box, for
>> > this i used another option given in Amber program such as ambpdb to save
>> > coordinates but it also show to much variable coordinates , specially in
>> > negative values. What is going wrong, Please help me in this regard.
>> >
>>
>> ?This is natural -- you would expect individual solvent molecules to drift
>> out of the unit cell from which they started. But keep in mind that with
>> periodic boundary conditions, when a particle drifts out of a particular
>> unit cell, another of its periodic images drifts in on the opposite side.
>>
>> This is simply a visualization artifact caused by the fact that we only
>> store the positions of *one* image of each particle (it's impossible to
>> store all infinity of them, obviously). You can use the "autoimage"
>> command in cpptraj to map everything back into a single unit cell if this
>> helps:
>>
>> trajin your_trajectory
>> autoimage
>> trajout imaged_trajectory
>>
>> Obviously change the names of the trajectory files to what you want.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> ------------------------------
>>
>> Message: 13
>> Date: Wed, 08 Jul 2015 14:31:46 +0100
>> From: Juan Eiros Zamora <j.eiros-zamora14.imperial.ac.uk>
>> Subject: Re: [AMBER] About python usage in AmberTools
>> To: amber.ambermd.org
>> Message-ID: <559D2642.6080004.imperial.ac.uk>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>> Dear Jason,
>>
>> I followed your instructions and managed to pass (almost all) of the
>> tests. Now if I want to use AmberTools python scripts I have to
>> previously activate the py27 conda environment? Or that was just for the
>> setup?
>>
>> I've tried several of the .py programs in the /bin/ directory and they
>> all seem to be working fine. But the mdout_analyzer.py script is
>> failing, giving the following error
>>
>> > (py27)je714:/usr/local/amber15/bin$ mdout_analyzer.py
>> > Traceback (most recent call last):
>> > File "/usr/local/amber15/bin/mdout_analyzer.py", line 3, in <module>
>> > from tkFileDialog import askopenfilenames
>> > File "/usr/local/lib/python2.7/lib-tk/tkFileDialog.py", line 43, in
>> > <module>
>> > from tkCommonDialog import Dialog
>> > File "/usr/local/lib/python2.7/lib-tk/tkCommonDialog.py", line 11,
>> > in <module>
>> > from Tkinter import *
>> > File "/usr/local/lib/python2.7/lib-tk/Tkinter.py", line 39, in
>> <module>
>> > import _tkinter # If this fails your Python may not be configured
>> > for Tk
>> > ImportError: No module named _tkinter
>>
>> But as you said earlier in the conversation, the Tkinter module is
>> installed by default in the conda distribution (why is it looking for
>> _tkinter by the way? that might be the issue)
>>
>> > (py27)je714:/usr/local/amber15/bin$ python
>> > Python 2.7.10 |Continuum Analytics, Inc.| (default, May 28 2015,
>> > 17:02:03)
>> > [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
>> > Type "help", "copyright", "credits" or "license" for more information.
>> > Anaconda is brought to you by Continuum Analytics.
>> > Please check out: http://continuum.io/thanks and https://binstar.org
>> > >>> import Tkinter
>>
>>
>> Additionally .Hai,
>>
>> I've succesfully installed pytraj from the github (had to 'export
>> CPPTRAJHOME=/home/je714/pytraj/cpptraj'
>> and 'export
>> LD_LIBRARY_PATH=/home/je714/pytraj/cpptraj/lib:$LD_LIBRARY_PATH' for it
>> to work though).
>>
>> Now, I get the batman logo saying "succesfully install pytraj" and "make
>> sure to add /home/je714/pytraj/cpptraj/lib/ to your LD_LIBRARY_PATH". I
>> do so but get the following error:
>>
>> > je714:/home/je714/pytraj$ python
>> > Python 3.4.3 |Anaconda 2.1.0 (64-bit)| (default, Jun 4 2015, 15:29:08)
>> > [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
>> > Type "help", "copyright", "credits" or "license" for more information.
>> > >>> import pytraj
>> > Traceback (most recent call last):
>> > File "<stdin>", line 1, in <module>
>> > File "/home/je714/pytraj/pytraj/__init__.py", line 19, in <module>
>> > from .core import Atom, Residue, Molecule
>> > File "/home/je714/pytraj/pytraj/core/__init__.py", line 2, in <module>
>> > from .Atom import Atom
>> > ImportError: No module named 'pytraj.core.Atom'
>>
>> Any ideas on what might be wrong here? (Also note I did the installation
>> for my Python 3.4 conda environment)
>>
>> Sorry for the long e-mail, but I think it's best that I ask my two
>> questions instead of replying two times.
>>
>> All the best,
>>
>> Juan
>>
>> On 07/07/15 20:54, Jason Swails wrote:
>> > On Tue, Jul 7, 2015 at 3:50 PM, Eiros Zamora, Juan <
>> > j.eiros-zamora14.imperial.ac.uk> wrote:
>> >
>> >> Hi Jason,
>> >>
>> >> So once I've created the environment py27 with conda, how do I use it
>> with
>> >> Amber?
>> >>
>> > ?You need to activate that environment:
>> >
>> > source activate py27
>> >
>> > Then AmberTools' configure should pick up that Python (as long as that's
>> > the python that is run when you just type "python" in the terminal).
>> > configure should output the Python that it finds and decides to use.
>> >
>> > HTH,
>> > Jason
>> >
>>
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 14
>> Date: Wed, 8 Jul 2015 09:59:11 -0400
>> From: Jason Swails <jason.swails.gmail.com>
>> Subject: Re: [AMBER] About python usage in AmberTools
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAEk9e3o=
>> WYLPifH+D3-v7AZY2SgQXLPYej9K7fRjKz35-DxTNA.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> On Wed, Jul 8, 2015 at 9:31 AM, Juan Eiros Zamora <
>> j.eiros-zamora14.imperial.ac.uk> wrote:
>>
>> > Dear Jason,
>> >
>> > I followed your instructions and managed to pass (almost all) of the
>> > tests. Now if I want to use AmberTools python scripts I have to
>> > previously activate the py27 conda environment? Or that was just for the
>> > setup?
>> >
>>
>> ?Yes, you need to activate the py27 conda environment.
>> ?
>>
>>
>> >
>> > I've tried several of the .py programs in the /bin/ directory and they
>> > all seem to be working fine. But the mdout_analyzer.py script is
>> > failing, giving the following error
>> >
>> > > (py27)je714:/usr/local/amber15/bin$ mdout_analyzer.py
>> > > Traceback (most recent call last):
>> > > File "/usr/local/amber15/bin/mdout_analyzer.py", line 3, in <module>
>> > > from tkFileDialog import askopenfilenames
>> > > File "/usr/local/lib/python2.7/lib-tk/tkFileDialog.py", line 43, in
>> > > <module>
>> > > from tkCommonDialog import Dialog
>> > > File "/usr/local/lib/python2.7/lib-tk/tkCommonDialog.py", line 11,
>> > > in <module>
>> > > from Tkinter import *
>> > > File "/usr/local/lib/python2.7/lib-tk/Tkinter.py", line 39, in
>> <module>
>> > > import _tkinter # If this fails your Python may not be configured
>> > > for Tk
>> > > ImportError: No module named _tkinter
>> >
>> > But as you said earlier in the conversation, the Tkinter module is
>> > installed by default in the conda distribution (why is it looking for
>> > _tkinter by the way? that might be the issue)
>> >
>>
>> ?_tkinter is the C-compiled extension module -- it's necessary. Look at
>> the head of mdout_analyzer.py in $AMBERHOME/bin. It's looking for the
>> libraries in /usr/local/lib/python2.7, not whatever your conda install
>> would normally be. I suspect that the Python interpreter in the
>> mdout_analyzer.py shebang line is not your conda py27 env version, but
>> instead /usr/local/bin/python2.7 (or something like that). Which would
>> seem to suggest that mdout_analyzer.py didn't get properly reinstalled
>> after you reconfigured with the --with-python flag.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> ------------------------------
>>
>> Message: 15
>> Date: Wed, 08 Jul 2015 15:19:02 +0100
>> From: Juan Eiros Zamora <j.eiros-zamora14.imperial.ac.uk>
>> Subject: Re: [AMBER] About python usage in AmberTools
>> To: amber.ambermd.org
>> Message-ID: <559D3156.3020606.imperial.ac.uk>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>> Hi Jason,
>> > Which would
>> > seem to suggest that mdout_analyzer.py didn't get properly reinstalled
>> > after you reconfigured with the --with-python flag.
>> >
>> > HTH,
>> > Jason
>> >
>> I did not use that flag, all I did was create the py27 conda
>> environment, activate it and run the ./configure gnu script. I'll try to
>> start from scratch using that flag then. My bad.
>>
>> All the best,
>>
>> Juan
>>
>>
>>
>> ------------------------------
>>
>> Message: 16
>> Date: Wed, 8 Jul 2015 10:20:13 -0400
>> From: Jason Swails <jason.swails.gmail.com>
>> Subject: Re: [AMBER] About python usage in AmberTools
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <
>> CAEk9e3oK9zGyQYurqzriQVRON0hFi6LPo4i2cnS1WvO6NhTrzw.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> On Wed, Jul 8, 2015 at 10:19 AM, Juan Eiros Zamora <
>> j.eiros-zamora14.imperial.ac.uk> wrote:
>>
>> > Hi Jason,
>> > > Which would
>> > > seem to suggest that mdout_analyzer.py didn't get properly reinstalled
>> > > after you reconfigured with the --with-python flag.
>> > >
>> > > HTH,
>> > > Jason
>> > >
>> > I did not use that flag, all I did was create the py27 conda
>> > environment, activate it and run the ./configure gnu script. I'll try to
>> > start from scratch using that flag then. My bad.
>> >
>>
>> ?Not necessarily a mistake. Look at config.h and search for the PYTHON
>> variable. What does it point to?
>>
>> ?
>>
>>
>> >
>> > All the best,
>> >
>> > Juan
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> ------------------------------
>>
>> Message: 17
>> Date: Wed, 8 Jul 2015 16:20:56 +0200
>> From: giulia palermo <giulia.palermo83.gmail.com>
>> Subject: Re: [AMBER] Paramentrization of a Uracil base with an O3'
>> terminus deprotonated.
>> To: AMBER Mailing List <amber.ambermd.org>, Lorenzo Casalino
>> <lcasalino.sissa.it>
>> Message-ID:
>> <CAHde_OaNdRqd=YyTdH1S1WOibRmLOCfMOzA+Df=
>> JvgrLNtK2NA.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear Jason,
>>
>> thank you for your e-mail and sorry if I have not clearly explained my
>> problem.
>> Our Uracile has to be deprotonated at O3' in order to exert a specific
>> mechanism.
>>
>> Thus, we are calculating the RESP charges for a deprotonated Uracile.
>> We have already parametrized nucleic acid bases using the capping
>> procedure.
>> At that time, we have employed a methyl group for capping O5' and H for
>> capping O3'.
>> In this way, the TOTAL charge of the capping residues is ZERO.
>>
>> In the case of a deprotonated Uracile, we can not cap O5' with a methyl
>> group. Indeed, the total charge of the methyl is 0.188 (NOT ZERO) and
>> during the refitting procedure, we would end up with a spurious charge,
>> because the TOTAL charge of the capping residues will not be zero.
>>
>> How do you suggest to cap the O5' ??
>>
>>
>> Thank you
>> g & l.
>>
>>
>>
>>
>> 2015-07-08 15:11 GMT+02:00 Jason Swails <jason.swails.gmail.com>:
>>
>> > On Wed, Jul 8, 2015 at 4:14 AM, giulia palermo <
>> giulia.palermo83.gmail.com
>> > >
>> > wrote:
>> >
>> > > Dear all,
>> > >
>> > > we am parametrizing a Uracil base with an O3' terminus deprotonated.
>> > >
>> > > As specified by the AMBER tutorial and done by Cornell et al. JACS
>> 117,
>> > > 1195, during the derivation of the Electrostatic Potential via QM
>> > > calculations, a methyl group is used for the capping of the O5', while
>> > the
>> > > O3' is capped with an hydrogen atom.
>> > > Subsequently, during the RESP fitting procedure, the TOTAL charge of
>> the
>> > > capping metyl (.O5') and of the hydrogen (.O3') is set to ZERO.
>> > >
>> > > In our case, this can not be done, because the O3' terminus should be
>> > > deprotonated.
>> > > How do you suggest to proceed in such a way?
>> > >
>> >
>> > ?The basic approach is to use capping groups to make sure you actually
>> run
>> > a QM calculation on a full molecule (not one with missing atoms and
>> > dangling bonds -- that makes no sense in a QM calculation). However,
>> you
>> > never want the capping group to "steal" charge from the assigned partial
>> > atomic charges of the fragment (since then you will wind up with a
>> > non-integer charge). So when fitting charges, you apply the constraint
>> > that the added fragments must carry a net neutral charge. This will
>> make
>> > sure that the fragment has the full charge you want.
>> >
>> > It's not entirely clear why you say "this cannot be done because the O3'
>> > terminus should be deprotonated". The net charge of all atoms you add
>> to
>> > your fragment should be constrained to zero. If you are simulating a
>> > deprotonated 3' terminus, then your net charge on the QM region should
>> be
>> > -2, but the constraint on the added methyl group (and any other added
>> atom)
>> > should still be 0.
>> >
>> > Or maybe I didn't understand your question/problem?
>> >
>> > HTH,
>> > Jason
>> >
>> > --
>> > Jason M. Swails
>> > BioMaPS,
>> > Rutgers University
>> > Postdoctoral Researcher
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> ------------------------------
>>
>> Message: 18
>> Date: Wed, 08 Jul 2015 15:26:35 +0100
>> From: Juan Eiros Zamora <j.eiros-zamora14.imperial.ac.uk>
>> Subject: Re: [AMBER] About python usage in AmberTools
>> To: amber.ambermd.org
>> Message-ID: <559D331B.5010002.imperial.ac.uk>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>>
>> > ?Not necessarily a mistake. Look at config.h and search for the PYTHON
>> > variable. What does it point to?
>> >
>> 192 #Python interpreter we are using
>> 193 PYTHON=/home/je714/anaconda3/envs/py27/bin/python2.7
>> 194
>> 195 #Type of Amber_Phenix build and python include file
>> 196 AMBERPHENIX=no
>> 197 INCLUDE_PY=/home/je714/anaconda3/envs/py27/include/python2.7
>> 198 PYTHON_VER=2.7
>> 199 PHENIX_INC=
>> 200 PHENIX_REPO=
>>
>> So it seems to have picked it up correctly.
>>
>> But the first line of the mdout_analyzer.py script is setting up a wrong
>> python I think:
>>
>> #!/usr/local/bin/python2.7
>>
>>
>>
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 19
>> Date: Wed, 8 Jul 2015 12:37:20 -0400
>> From: Hai Nguyen <nhai.qn.gmail.com>
>> Subject: Re: [AMBER] About python usage in AmberTools
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <
>> CAFNMPM-FBP_vhz-SeS3OC0rmkrvTRTBQBcwwAFk4fsb6qVg2Qg.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> hi,
>>
>> you are staying in the source code folder. So when you `import pytraj`,
>> python try to import "/home/je714/pytraj/pytraj/". If you are using
>> ananconda, installed pytraj should be in /home/anaconda3 (or
>> /home/ananconda/)
>>
>> Try to "cd tests" and then "python ./run_simple_test.py" to run. (or run
>> any test file in that folder).
>>
>> or "cd /home/" and try to import pytraj again. I will add checking to
>> pytraj to have more warning. thanks
>>
>> Hai
>>
>> On Wed, Jul 8, 2015 at 9:31 AM, Juan Eiros Zamora <
>> j.eiros-zamora14.imperial.ac.uk> wrote
>> >
>> > Additionally .Hai,
>> >
>> > I've succesfully installed pytraj from the github (had to 'export
>> > CPPTRAJHOME=/home/je714/pytraj/cpptraj'
>> > and 'export
>> > LD_LIBRARY_PATH=/home/je714/pytraj/cpptraj/lib:$LD_LIBRARY_PATH' for it
>> > to work though).
>> >
>> > Now, I get the batman logo saying "succesfully install pytraj" and "make
>> > sure to add /home/je714/pytraj/cpptraj/lib/ to your LD_LIBRARY_PATH". I
>> > do so but get the following error:
>> >
>> > > je714:/home/je714/pytraj$ python
>> > > Python 3.4.3 |Anaconda 2.1.0 (64-bit)| (default, Jun 4 2015,
>> 15:29:08)
>> > > [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
>> > > Type "help", "copyright", "credits" or "license" for more information.
>> > > >>> import pytraj
>> > > Traceback (most recent call last):
>> > > File "<stdin>", line 1, in <module>
>> > > File "/home/je714/pytraj/pytraj/__init__.py", line 19, in <module>
>> > > from .core import Atom, Residue, Molecule
>> > > File "/home/je714/pytraj/pytraj/core/__init__.py", line 2, in
>> <module>
>> > > from .Atom import Atom
>> > > ImportError: No module named 'pytraj.core.Atom'
>> >
>> > Any ideas on what might be wrong here? (Also note I did the installation
>> > for my Python 3.4 conda environment)
>> >
>> > Sorry for the long e-mail, but I think it's best that I ask my two
>> > questions instead of replying two times.
>> >
>> > All the best,
>> >
>> > Juan
>> >
>> > On 07/07/15 20:54, Jason Swails wrote:
>> > > On Tue, Jul 7, 2015 at 3:50 PM, Eiros Zamora, Juan <
>> > > j.eiros-zamora14.imperial.ac.uk> wrote:
>> > >
>> > >> Hi Jason,
>> > >>
>> > >> So once I've created the environment py27 with conda, how do I use it
>> > with
>> > >> Amber?
>> > >>
>> > > ?You need to activate that environment:
>> > >
>> > > source activate py27
>> > >
>> > > Then AmberTools' configure should pick up that Python (as long as
>> that's
>> > > the python that is run when you just type "python" in the terminal).
>> > > configure should output the Python that it finds and decides to use.
>> > >
>> > > HTH,
>> > > Jason
>> > >
>> >
>> >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> ------------------------------
>>
>> Message: 20
>> Date: Wed, 8 Jul 2015 12:42:10 -0400
>> From: Hai Nguyen <nhai.qn.gmail.com>
>> Subject: Re: [AMBER] About python usage in AmberTools
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAFNMPM_5o1NqvUEmudzu4h9+rF8L=
>> 81dRiL61KYqi2hFndrjoQ.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> On Wed, Jul 8, 2015 at 10:26 AM, Juan Eiros Zamora <
>> j.eiros-zamora14.imperial.ac.uk> wrote:
>>
>> >
>> > > ?Not necessarily a mistake. Look at config.h and search for the
>> PYTHON
>> > > variable. What does it point to?
>> > >
>> > 192 #Python interpreter we are using
>> > 193 PYTHON=/home/je714/anaconda3/envs/py27/bin/python2.7
>> > 194
>> > 195 #Type of Amber_Phenix build and python include file
>> > 196 AMBERPHENIX=no
>> > 197 INCLUDE_PY=/home/je714/anaconda3/envs/py27/include/python2.7
>> > 198 PYTHON_VER=2.7
>> > 199 PHENIX_INC=
>> > 200 PHENIX_REPO=
>> >
>> > So it seems to have picked it up correctly.
>> >
>> > But the first line of the mdout_analyzer.py script is setting up a wrong
>> > python I think:
>> >
>> >
>>
>> > #!/usr/local/bin/python2.7
>> >
>> >
>> Yes I think this will use default python2.7. You can delete this line or
>> change to "#!/usr/bin/env python"
>>
>> Hai
>>
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > 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
>>
>>
>> End of AMBER Digest, Vol 1274, Issue 1
>> **************************************
>>
>
>
>
> --
> Mathematics, School of Physical Sciences
> Biological Sciences, School of Biological Sciences
> University of California: Irvine
>
> President, Anteaters Mathematics Club
> Advocacy Committee, Biological Sciences Student Council
>
>
>
--
Mathematics, School of Physical Sciences
Biological Sciences, School of Biological Sciences
University of California: Irvine
President, Anteaters Mathematics Club
Advocacy Committee, Biological Sciences Student Council
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 09 2015 - 15:30:02 PDT
