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
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> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 09 2015 - 14:30:02 PDT
