Re: [AMBER] AMBER Digest, Vol 1497, Issue 1

From: necmettin pirinccioglu <pirincn.gmail.com>
Date: Fri, 26 Feb 2016 15:21:53 +0200

Dear All,
I have been running MD for diphosphoric acid anion with the following input
but I get the error message below. Helps will be welcomed!

INPUT
 &cntrl
  imin=0, irest=1, ntx=5,
  nstlim=250000, dt=0.002,
  ntc=4, ntf=4,
  ntt=1, tautp=0.5,
  tempi=600.0, temp0=600.0,
  ntpr=500, ntwx=500,
  ntb=0, igb=0,
  cut=999
 /

ERROR MESSAGE!!!
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 1
| TOTAL SIZE OF NONBOND LIST = 1
vlimit exceeded for step 369; vmax = 22.0998
vlimit exceeded for step 373; vmax = 54.3352

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 0 1 1 2

--
Necmettin Pirinccioglu (BSc, PhD)
Department of Chemistry
University of Dicle
21280 Diyarbakir
TURKEY
------------------------------
Message: 9
Date: Thu, 25 Feb 2016 01:00:15 -0800
From: Ross Walker <ross.rosswalker.co.uk>
Subject: Re: [AMBER] problem running MD for diphosphoric acid anion
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <227AFD5C-E4F8-4D50-85CA-433B32C297B8.rosswalker.co.uk>
Content-Type: text/plain; charset=us-ascii
Hi Necmettin,
A few notes here. Firstly it is best to run a small number of steps say
nstlim=500 with ntwx and ntpr = 1. That way you can see in detail what is
going wrong and visualize the trajectory.
Also, tempi=600 is hot - that may causes issues - especially if your system
is not well equilibrated first.
Finally ntc=4, ntf=4 - I have no idea if this works / gives you a stable
potential function. I would not recommend going above ntf=2,ntc=2 for
anything other than debugging.
If changing to ntc=2,ntf=2 does not fix things then look carefully at your
structure - it may not be well enough minimized, it may have structural
deficiencies etc. Visualizing for and ntwx=1 run will help here.
The parameters may also be suspect since this is not a regular amino /
nucleic acid - where did you get the parameters from?
All the best
Ross
Dear Ross, thanks for your kind reply. well firstly i did try with
ntf=2,ntc=2 (the number 4 is for my last try) and secondly i have employed
a shorter period. the trajectories indicate that the structure collapses
and the mds are ended with the error after a while. please find the md
trajectories as attached. I have done these calculations even at 700 K but
it worked fine with other small moleculs. but i have just got this with
phosphoric acid. best wishes, necmettin
On Thu, Feb 25, 2016 at 10:00 PM, <amber-request.ambermd.org> wrote:
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>
> Today's Topics:
>
>    1. Re: R: Fwd: cpinutil.py problem (Jason Swails)
>    2. R:  R: Fwd: cpinutil.py problem (Elisa Pieri)
>    3. Thermodynamic Integration (Vertika Gautam)
>    4. Fwd: Thermodynamic Integration (Vertika Gautam)
>    5. Re: Fwd: Thermodynamic Integration (Nhai)
>    6. Re: Fwd: Thermodynamic Integration (David Cerutti)
>    7. Ph.D. position, Nancy, France (Gerald Monard)
>    8. problem running MD for diphosphoric acid anion
>       (necmettin pirinccioglu)
>    9. Re: problem running MD for diphosphoric acid anion (Ross Walker)
>   10. Re: parameter file for graphene oxide (Jesmita Dhar)
>   11. Re: parameter file for graphene oxide (Karl Kirschner)
>   12. Minimization error using Sander (Anna Cebrian Prats)
>   13. Re: Minimization error using Sander (Bill Ross)
>   14. Re: Minimization error using Sander (David A Case)
>   15. Maximum input value for the isothermal compressibility in
>       AMBER (BLEY Michael)
>   16. Re: Maximum input value for the isothermal compressibility in
>       AMBER (David A Case)
>   17. Re: Minimization error using Sander (Anna Cebrian Prats)
>   18. Question regarding protein-Dna binding free energy (Mahdieh Hadi)
>   19. Re: Question regarding protein-Dna binding free energy
>       (Vlad Cojocaru)
>   20. Re: Question regarding protein-Dna binding free energy
>       (Mahdieh Hadi)
>   21. Re: Question regarding protein-Dna binding free energy
>       (Vlad Cojocaru)
>   22. MMGBSA error (Indrajit Deb)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 24 Feb 2016 21:28:37 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] R: Fwd: cpinutil.py problem
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
>         <CAEk9e3pkWLMYQKENJ6rVy04-Yht=09=
> YiJajkre7-Ft9dpzHdw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> What tarball did you receive from me?
>
> On Wed, Feb 24, 2016 at 1:18 PM, Elisa Pieri <elisa.pieri90.gmail.com>
> wrote:
>
> > Hi Jason,
> >
> > The AmberTools15 I have has been downloaded from the amber website, and I
> > received the amber14 tarball from you. I am not expert enough to play
> with
> > github :)
> >
> > Tell me if you find something because I really need it.
> >
> > Thank you,
> > Elisa
> >
> > ----- Messaggio originale -----
> > Da: "Jason Swails" <jason.swails.gmail.com>
> > Inviato: ?24/?02/?2016 18:31
> > A: "AMBER Mailing List" <amber.ambermd.org>
> > Oggetto: Re: [AMBER] Fwd: cpinutil.py problem
> >
> >
> >
> > > On Feb 24, 2016, at 8:15 AM, Elisa Pieri <elisa.pieri90.gmail.com>
> > wrote:
> > >
> > > Jason: I tried compiling Amber in serial, but I got exactly the same
> > error.
> > >
> > > Marcelo: I did what you suggested, my amber.sh file looks exactly as
> > yours,
> > > but I still have the same problem.
> > >
> > > Anyway I have this problem with cpinutil.py only using the -op flag;
> > > without it, it works.
> > >
> > > Other ideas?
> >
> > Have you perhaps installed a newer version of ParmEd from Github?
> >
> > The cpinutil script in AmberTools 15 only works with ParmEd from
> > AmberTools 15. I'll try to dig up an AmberTools 15 release to see what
> > might be causing this problem, but I don't think you should get this
> error
> > if you are using just AmberTools 15 components... (And ParmEd from Github
> > shouldn't leak into AmberTools 15 applications anyway since the package
> > names were changed). So I'm really not sure how this is happening...
> >
> > > Elisa
> > >
> > > On Wed, Feb 24, 2016 at 4:26 AM, Marcelo Andrade Chagas <
> > > andrade.mchagas.gmail.com> wrote:
> > >
> > >> Hi
> > >>
> > >> I had a similar problem in python2.7 respectively scripts for
> > >> MCPB.py and parmed.py
> > >>
> > >> managed to solve AmberTools15  reinstalling as follows:
> > >>
> > >> First installed libraries missing:
> > >>
> > >> http://www.scipy.org/install.html
> > >>
> > >> sudo apt-get install python-numpy python-scipy python-matplotlib
> ipython
> > >> ipython-notebook python-pandas python-SymPy python-nose
> > >>
> > >> open your file and look for the error line I think it should be
> > something
> > >> like
> > >>
> > >> vi /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11
> > >>
> > >> do this before installing
> > >>
> > >> tar jxvf Amber14.tar.bz2
> > >>
> > >> export AMBERHOME=`pwd`
> > >>
> > >> ./configure --with-python /usr/bin/python2.7
> > >>
> > >> source amber.sh
> > >>
> > >> make install
> > >>
> > >> make test
> > >>
> > >> The following command to install in parallel (requires first install
> mpi
> > >> with the same compiler gnu)
> > >>
> > >> ./configure --with-python /usr/bin/python2.7 -mpi gnu
> > >>
> > >> make install
> > >>
> > >> then it was just to set the bash file contents amber.sh
> > >>
> > >> In my case:
> > >>
> > >> export AMBERHOME = "/ home / Marcelo / PROGRAMS / AMBER-NEW / amber14"
> > >> export PATH = "$ {AMBERHOME} / bin: $ {PATH}"
> > >>
> > >> # Add location of Amber Python modules to default Python search path
> > >> if [-z "$ PYTHONPATH ']; Then
> > >>    export PYTHONPATH = "$ {} AMBERHOME /lib/python2.7/site-packages"
> > >> else
> > >>    export PYTHONPATH = "$ {} AMBERHOME /lib/python2.7/site-packages: $
> > >> {PYTHONPATH}"
> > >> fi
> > >> if [-z "$ {LD_LIBRARY_PATH}"]; Then
> > >>   export LD_LIBRARY_PATH = "$ {AMBERHOME} /lib"
> > >> else
> > >>   export LD_LIBRARY_PATH = "$ {AMBERHOME} /lib: $ {LD_LIBRARY_PATH}"
> > >> fi
> > >>
> > >>
> > >> The problem in my case it was because they lacked python files and to
> > set
> > >> needed which seek python2.7
> > >>
> > >> Best regards
> > >>
> > >> Marcelo
> > >>
> > >>
> > >> Marcelo Andrade Chagas, MSc
> > >> (PhD student)
> > >> Laborat?rio de Qu?mica Computacional e Modelagem Molecular - LQC-MM
> > >> * http://lqcmm.qui.ufmg.br/
> > >> Departamento de Qu?mica da Universidade Federal de Minas Gerais - UFMG
> > >> Tel:(31)3409-5776
> > >>
> > >> 2016-02-23 12:39 GMT-03:00 Elisa Pieri <elisa.pieri90.gmail.com>:
> > >>
> > >>> Hi everybody,
> > >>>
> > >>> I have Amber14, but when I use the command
> > >>>
> > >>> cpinutil.py -p crys.solv10.parm7 -igb 2 -o crys.solv10.cpin -op
> > >>> crys.solv10.modO.parm7 -resnames AS4 GL4 HIP
> > >>>
> > >>> I get this error:
> > >>>
> > >>> /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11:
> > >>> ModuleDeprecationWarning: The oldnumeric module will be dropped in
> > Numpy
> > >>> 1.9
> > >>>  warnings.warn(_msg, ModuleDeprecationWarning)
> > >>> Traceback (most recent call last):
> > >>>  File "/home/elisa/amber14/bin/cpinutil.py", line 289, in <module>
> > >>>    main(opt)
> > >>>  File "/home/elisa/amber14/bin/cpinutil.py", line 256, in main
> > >>>    changeradii(parm, 'mbondi2').execute()
> > >>> NameError: global name 'changeradii' is not defined
> > >>>
> > >>> and OC crys.solv10.modO.parm7 is not produced. What's happening?
> > >>>
> > >>> Elisa
> > >>> _______________________________________________
> > >>> 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
> > > _______________________________________________
> > > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 25 Feb 2016 07:33:45 +0100
> From: Elisa Pieri <elisa.pieri90.gmail.com>
> Subject: [AMBER] R:  R: Fwd: cpinutil.py problem
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <56cea04f.8e301c0a.9872e.6a83.mx.google.com>
> Content-Type: text/plain; charset="utf-8"
>
> Sorry, I wasn't clear, "you" means the Amber Organization (after the
> payment of My university :D)!
>
> Elisa
>
> ----- Messaggio originale -----
> Da: "Jason Swails" <jason.swails.gmail.com>
> Inviato: ?25/?02/?2016 03:28
> A: "AMBER Mailing List" <amber.ambermd.org>
> Oggetto: Re: [AMBER] R: Fwd: cpinutil.py problem
>
> What tarball did you receive from me?
>
> On Wed, Feb 24, 2016 at 1:18 PM, Elisa Pieri <elisa.pieri90.gmail.com>
> wrote:
>
> > Hi Jason,
> >
> > The AmberTools15 I have has been downloaded from the amber website, and I
> > received the amber14 tarball from you. I am not expert enough to play
> with
> > github :)
> >
> > Tell me if you find something because I really need it.
> >
> > Thank you,
> > Elisa
> >
> > ----- Messaggio originale -----
> > Da: "Jason Swails" <jason.swails.gmail.com>
> > Inviato: ?24/?02/?2016 18:31
> > A: "AMBER Mailing List" <amber.ambermd.org>
> > Oggetto: Re: [AMBER] Fwd: cpinutil.py problem
> >
> >
> >
> > > On Feb 24, 2016, at 8:15 AM, Elisa Pieri <elisa.pieri90.gmail.com>
> > wrote:
> > >
> > > Jason: I tried compiling Amber in serial, but I got exactly the same
> > error.
> > >
> > > Marcelo: I did what you suggested, my amber.sh file looks exactly as
> > yours,
> > > but I still have the same problem.
> > >
> > > Anyway I have this problem with cpinutil.py only using the -op flag;
> > > without it, it works.
> > >
> > > Other ideas?
> >
> > Have you perhaps installed a newer version of ParmEd from Github?
> >
> > The cpinutil script in AmberTools 15 only works with ParmEd from
> > AmberTools 15. I'll try to dig up an AmberTools 15 release to see what
> > might be causing this problem, but I don't think you should get this
> error
> > if you are using just AmberTools 15 components... (And ParmEd from Github
> > shouldn't leak into AmberTools 15 applications anyway since the package
> > names were changed). So I'm really not sure how this is happening...
> >
> > > Elisa
> > >
> > > On Wed, Feb 24, 2016 at 4:26 AM, Marcelo Andrade Chagas <
> > > andrade.mchagas.gmail.com> wrote:
> > >
> > >> Hi
> > >>
> > >> I had a similar problem in python2.7 respectively scripts for
> > >> MCPB.py and parmed.py
> > >>
> > >> managed to solve AmberTools15  reinstalling as follows:
> > >>
> > >> First installed libraries missing:
> > >>
> > >> http://www.scipy.org/install.html
> > >>
> > >> sudo apt-get install python-numpy python-scipy python-matplotlib
> ipython
> > >> ipython-notebook python-pandas python-SymPy python-nose
> > >>
> > >> open your file and look for the error line I think it should be
> > something
> > >> like
> > >>
> > >> vi /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11
> > >>
> > >> do this before installing
> > >>
> > >> tar jxvf Amber14.tar.bz2
> > >>
> > >> export AMBERHOME=`pwd`
> > >>
> > >> ./configure --with-python /usr/bin/python2.7
> > >>
> > >> source amber.sh
> > >>
> > >> make install
> > >>
> > >> make test
> > >>
> > >> The following command to install in parallel (requires first install
> mpi
> > >> with the same compiler gnu)
> > >>
> > >> ./configure --with-python /usr/bin/python2.7 -mpi gnu
> > >>
> > >> make install
> > >>
> > >> then it was just to set the bash file contents amber.sh
> > >>
> > >> In my case:
> > >>
> > >> export AMBERHOME = "/ home / Marcelo / PROGRAMS / AMBER-NEW / amber14"
> > >> export PATH = "$ {AMBERHOME} / bin: $ {PATH}"
> > >>
> > >> # Add location of Amber Python modules to default Python search path
> > >> if [-z "$ PYTHONPATH ']; Then
> > >>    export PYTHONPATH = "$ {} AMBERHOME /lib/python2.7/site-packages"
> > >> else
> > >>    export PYTHONPATH = "$ {} AMBERHOME /lib/python2.7/site-packages: $
> > >> {PYTHONPATH}"
> > >> fi
> > >> if [-z "$ {LD_LIBRARY_PATH}"]; Then
> > >>   export LD_LIBRARY_PATH = "$ {AMBERHOME} /lib"
> > >> else
> > >>   export LD_LIBRARY_PATH = "$ {AMBERHOME} /lib: $ {LD_LIBRARY_PATH}"
> > >> fi
> > >>
> > >>
> > >> The problem in my case it was because they lacked python files and to
> > set
> > >> needed which seek python2.7
> > >>
> > >> Best regards
> > >>
> > >> Marcelo
> > >>
> > >>
> > >> Marcelo Andrade Chagas, MSc
> > >> (PhD student)
> > >> Laborat?rio de Qu?mica Computacional e Modelagem Molecular - LQC-MM
> > >> * http://lqcmm.qui.ufmg.br/
> > >> Departamento de Qu?mica da Universidade Federal de Minas Gerais - UFMG
> > >> Tel:(31)3409-5776
> > >>
> > >> 2016-02-23 12:39 GMT-03:00 Elisa Pieri <elisa.pieri90.gmail.com>:
> > >>
> > >>> Hi everybody,
> > >>>
> > >>> I have Amber14, but when I use the command
> > >>>
> > >>> cpinutil.py -p crys.solv10.parm7 -igb 2 -o crys.solv10.cpin -op
> > >>> crys.solv10.modO.parm7 -resnames AS4 GL4 HIP
> > >>>
> > >>> I get this error:
> > >>>
> > >>> /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11:
> > >>> ModuleDeprecationWarning: The oldnumeric module will be dropped in
> > Numpy
> > >>> 1.9
> > >>>  warnings.warn(_msg, ModuleDeprecationWarning)
> > >>> Traceback (most recent call last):
> > >>>  File "/home/elisa/amber14/bin/cpinutil.py", line 289, in <module>
> > >>>    main(opt)
> > >>>  File "/home/elisa/amber14/bin/cpinutil.py", line 256, in main
> > >>>    changeradii(parm, 'mbondi2').execute()
> > >>> NameError: global name 'changeradii' is not defined
> > >>>
> > >>> and OC crys.solv10.modO.parm7 is not produced. What's happening?
> > >>>
> > >>> Elisa
> > >>> _______________________________________________
> > >>> 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
> > > _______________________________________________
> > > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 25 Feb 2016 14:44:05 +0800
> From: Vertika Gautam <vartikapisces.gmail.com>
> Subject: [AMBER] Thermodynamic Integration
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
>         <
> CAD2fjZeZ5pyhbQfaaK_zHfgFe-3NhRamqN8c+XSepkFJEC0pcw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear All,
>
> I want to compare two Ankyrin proteins (almost similar but one of the
> Ankyrin with one extra loop) for their binding towards the same receptor.
> Is it possible to do?
>
>
>
> Thanks
>
> --
> Vertika Gautam
>
> Research Assistant
> Drug Design and Development Research Group (DDDRG)
> Department of Chemistry, Faculty of Science
> University of Malaya
>
>
>
> *e-mail address: vartikapisces.gmail.com
> <vartikapisces.gmail.com>
> vartikapisces.hotmail.com <vartikapisces.hotmail.com>
>     01112294191*
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 25 Feb 2016 14:49:25 +0800
> From: Vertika Gautam <vartikapisces.gmail.com>
> Subject: [AMBER] Fwd: Thermodynamic Integration
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
>         <CAD2fjZdjP3HObJz9+OWQY=
> r8Gr0taxJUa0soV-yra7WHDGj+dQ.mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> ---------- Forwarded message ----------
> From: Vertika Gautam <vartikapisces.gmail.com>
> Date: Thu, Feb 25, 2016 at 2:44 PM
> Subject: Thermodynamic Integration
> To: AMBER Mailing List <amber.ambermd.org>
>
>
> Dear All,
>
> I want to compare two Ankyrin proteins (almost similar but one of the
> Ankyrin with one extra loop) for their binding towards the same receptor.
> Is it possible to do?
>
> PS: for the convinience sequence alignment of two Ankyrins is attached
> herewith.
>
>
> Thanks
>
> --
> Vertika Gautam
>
> Research Assistant
> Drug Design and Development Research Group (DDDRG)
> Department of Chemistry, Faculty of Science
> University of Malaya
>
>
>
> *e-mail address: vartikapisces.gmail.com
> <vartikapisces.gmail.com>
> vartikapisces.hotmail.com <vartikapisces.hotmail.com>
>     01112294191*
>
>
>
> --
> Vertika Gautam
>
> Research Assistant
> Drug Design and Development Research Group (DDDRG)
> Department of Chemistry, Faculty of Science
> University of Malaya
>
>
>
> *e-mail address: vartikapisces.gmail.com
> <vartikapisces.gmail.com>
> vartikapisces.hotmail.com <vartikapisces.hotmail.com>
>     01112294191*
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: sequence alignment.docx
> Type:
> application/vnd.openxmlformats-officedocument.wordprocessingml.document
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> Desc: not available
> Url :
> http://lists.ambermd.org/mailman/private/amber/attachments/20160225/573e7636/attachment-0001.bin
>
> ------------------------------
>
> Message: 5
> Date: Thu, 25 Feb 2016 01:58:50 -0500
> From: Nhai <nhai.qn.gmail.com>
> Subject: Re: [AMBER] Fwd: Thermodynamic Integration
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <7894623C-BCE6-412F-92A4-6C39CF3458ED.gmail.com>
> Content-Type: text/plain;       charset=us-ascii
>
> Hi
>
> Please be patient.
>
> Hai
>
> > On Feb 25, 2016, at 1:49 AM, Vertika Gautam <vartikapisces.gmail.com>
> wrote:
> >
> > ---------- Forwarded message ----------
> > From: Vertika Gautam <vartikapisces.gmail.com>
> > Date: Thu, Feb 25, 2016 at 2:44 PM
> > Subject: Thermodynamic Integration
> > To: AMBER Mailing List <amber.ambermd.org>
> >
> >
> > Dear All,
> >
> > I want to compare two Ankyrin proteins (almost similar but one of the
> > Ankyrin with one extra loop) for their binding towards the same receptor.
> > Is it possible to do?
> >
> > PS: for the convinience sequence alignment of two Ankyrins is attached
> > herewith.
> >
> >
> > Thanks
> >
> > --
> > Vertika Gautam
> >
> > Research Assistant
> > Drug Design and Development Research Group (DDDRG)
> > Department of Chemistry, Faculty of Science
> > University of Malaya
> >
> >
> >
> > *e-mail address: vartikapisces.gmail.com
> > <vartikapisces.gmail.com>
> > vartikapisces.hotmail.com <vartikapisces.hotmail.com>
> >    01112294191*
> >
> >
> >
> > --
> > Vertika Gautam
> >
> > Research Assistant
> > Drug Design and Development Research Group (DDDRG)
> > Department of Chemistry, Faculty of Science
> > University of Malaya
> >
> >
> >
> > *e-mail address: vartikapisces.gmail.com
> > <vartikapisces.gmail.com>
> > vartikapisces.hotmail.com <vartikapisces.hotmail.com>
> >    01112294191*
> > <sequence alignment.docx>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 25 Feb 2016 02:45:09 -0500
> From: David Cerutti <dscerutti.gmail.com>
> Subject: Re: [AMBER] Fwd: Thermodynamic Integration
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
>         <CAEmzWj20_YiVTysfs3tKd7cG=
> dAa9O56pY-CkoL+FTwN+tNtyg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Protein::protein binding is a tremendously hard problem, from a sampling
> point of view.  The potentials are pretty good, but it sounds almost like a
> delta G of folding calculation to bring two proteins into a docked pose and
> then pull them apart.  I was having a discussion earlier about the extent
> of our functionality in Amber, but the CHARMM community has a very clever
> method for implementing a harmonic restraint in the contact score (I'd
> imagine the algebra is really tedious) to run one-dimensional umbrella
> sampling calculations at various degrees of protein folding.  You should be
> able to leverage that sort of contact score to define bound and unbound
> states of your two proteins.
>
> See one of their papers:
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.24004/full
>
> Good luck!
>
> Dave
>
>
> On Thu, Feb 25, 2016 at 1:58 AM, Nhai <nhai.qn.gmail.com> wrote:
>
> > Hi
> >
> > Please be patient.
> >
> > Hai
> >
> > > On Feb 25, 2016, at 1:49 AM, Vertika Gautam <vartikapisces.gmail.com>
> > wrote:
> > >
> > > ---------- Forwarded message ----------
> > > From: Vertika Gautam <vartikapisces.gmail.com>
> > > Date: Thu, Feb 25, 2016 at 2:44 PM
> > > Subject: Thermodynamic Integration
> > > To: AMBER Mailing List <amber.ambermd.org>
> > >
> > >
> > > Dear All,
> > >
> > > I want to compare two Ankyrin proteins (almost similar but one of the
> > > Ankyrin with one extra loop) for their binding towards the same
> receptor.
> > > Is it possible to do?
> > >
> > > PS: for the convinience sequence alignment of two Ankyrins is attached
> > > herewith.
> > >
> > >
> > > Thanks
> > >
> > > --
> > > Vertika Gautam
> > >
> > > Research Assistant
> > > Drug Design and Development Research Group (DDDRG)
> > > Department of Chemistry, Faculty of Science
> > > University of Malaya
> > >
> > >
> > >
> > > *e-mail address: vartikapisces.gmail.com
> > > <vartikapisces.gmail.com>
> > > vartikapisces.hotmail.com <vartikapisces.hotmail.com>
> > >    01112294191*
> > >
> > >
> > >
> > > --
> > > Vertika Gautam
> > >
> > > Research Assistant
> > > Drug Design and Development Research Group (DDDRG)
> > > Department of Chemistry, Faculty of Science
> > > University of Malaya
> > >
> > >
> > >
> > > *e-mail address: vartikapisces.gmail.com
> > > <vartikapisces.gmail.com>
> > > vartikapisces.hotmail.com <vartikapisces.hotmail.com>
> > >    01112294191*
> > > <sequence alignment.docx>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 25 Feb 2016 09:39:31 +0100
> From: Gerald Monard <Gerald.Monard.univ-lorraine.fr>
> Subject: [AMBER] Ph.D. position, Nancy, France
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <56CEBDC3.4050105.univ-lorraine.fr>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
>
> Please find enclosed an announcement for an open PhD position in Nancy,
> France entitled "Modeling the structure and the dynamics of peptides and
> proteins in aqueous solution using novel semiempirical quantum methods".
>
> The work is targeted to start in Fall 2016, but application deadline is
> end of April. We are looking for good candidates with a background in
> computational chemistry, physics or biology. Experience in programming
> and numerical analysis are of advantage.
>
> Sincerely,
>
> Gerald.
>
> P.S.: French speaking is not required to apply for the position.
> --
>
> ____________________________________________________________________________
>
>   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
>
>
> ____________________________________________________________________________
>
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: Thesis-sebomd.pdf
> Type: application/force-download
> Size: 36113 bytes
> Desc: not available
> Url :
> http://lists.ambermd.org/mailman/private/amber/attachments/20160225/fa52dc65/attachment-0001.bin
>
> ------------------------------
>
> Message: 8
> Date: Thu, 25 Feb 2016 10:48:45 +0200
> From: necmettin pirinccioglu <pirincn.gmail.com>
> Subject: [AMBER] problem running MD for diphosphoric acid anion
> To: AMBER Mailing List <AMBER.ambermd.org>
> Message-ID:
>         <CAJ_uLzF8TyJpgVZooS=7JwzQcMSQq2Xx-UyAcSPfK5C_=
> bCk5w.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear All,
> I have been running MD for diphosphoric acid anion with the following input
> but I get the error message below. Helps will be welcomed!
>
> INPUT
>  &cntrl
>   imin=0, irest=1, ntx=5,
>   nstlim=250000, dt=0.002,
>   ntc=4, ntf=4,
>   ntt=1, tautp=0.5,
>   tempi=600.0, temp0=600.0,
>   ntpr=500, ntwx=500,
>   ntb=0, igb=0,
>   cut=999
>  /
>
> ERROR MESSAGE!!!
>  ---------------------------------------------------
> | Local SIZE OF NONBOND LIST =          1
> | TOTAL SIZE OF NONBOND LIST =          1
> vlimit exceeded for step    369; vmax =    22.0998
> vlimit exceeded for step    373; vmax =    54.3352
>
>      Coordinate resetting (SHAKE) cannot be accomplished,
>      deviation is too large
>      NITER, NIT, LL, I and J are :      0      0      1      1      2
>
> --
> Necmettin Pirinccioglu (BSc, PhD)
> Department of Chemistry
> University of Dicle
> 21280 Diyarbakir
> TURKEY
>
>
> ------------------------------
>
> Message: 9
> Date: Thu, 25 Feb 2016 01:00:15 -0800
> From: Ross Walker <ross.rosswalker.co.uk>
> Subject: Re: [AMBER] problem running MD for diphosphoric acid anion
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <227AFD5C-E4F8-4D50-85CA-433B32C297B8.rosswalker.co.uk>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Necmettin,
>
> A few notes here. Firstly it is best to run a small number of steps say
> nstlim=500 with ntwx and ntpr = 1. That way you can see in detail what is
> going wrong and visualize the trajectory.
>
> Also, tempi=600 is hot - that may causes issues - especially if your
> system is not well equilibrated first.
>
> Finally ntc=4, ntf=4 - I have no idea if this works / gives you a stable
> potential function. I would not recommend going above ntf=2,ntc=2 for
> anything other than debugging.
>
> If changing to ntc=2,ntf=2 does not fix things then look carefully at your
> structure - it may not be well enough minimized, it may have structural
> deficiencies etc. Visualizing for and ntwx=1 run will help here.
>
> The parameters may also be suspect since this is not a regular amino /
> nucleic acid - where did you get the parameters from?
>
> All the best
> Ross
>
> > On Feb 25, 2016, at 00:48, necmettin pirinccioglu <pirincn.gmail.com>
> wrote:
> >
> > Dear All,
> > I have been running MD for diphosphoric acid anion with the following
> input
> > but I get the error message below. Helps will be welcomed!
> >
> > INPUT
> > &cntrl
> >  imin=0, irest=1, ntx=5,
> >  nstlim=250000, dt=0.002,
> >  ntc=4, ntf=4,
> >  ntt=1, tautp=0.5,
> >  tempi=600.0, temp0=600.0,
> >  ntpr=500, ntwx=500,
> >  ntb=0, igb=0,
> >  cut=999
> > /
> >
> > ERROR MESSAGE!!!
> > ---------------------------------------------------
> > | Local SIZE OF NONBOND LIST =          1
> > | TOTAL SIZE OF NONBOND LIST =          1
> > vlimit exceeded for step    369; vmax =    22.0998
> > vlimit exceeded for step    373; vmax =    54.3352
> >
> >     Coordinate resetting (SHAKE) cannot be accomplished,
> >     deviation is too large
> >     NITER, NIT, LL, I and J are :      0      0      1      1      2
> >
> > --
> > Necmettin Pirinccioglu (BSc, PhD)
> > Department of Chemistry
> > University of Dicle
> > 21280 Diyarbakir
> > TURKEY
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 10
> Date: Thu, 25 Feb 2016 15:06:57 +0530
> From: Jesmita Dhar <dhar.beauty.gmail.com>
> Subject: Re: [AMBER] parameter file for graphene oxide
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
>         <CAMS2ayq=
> xNzMkMm_iVxP6XwMPHo3E9dZ-_yez-X3OU1cmL8pnw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hello,
> We are getting the following error while we have run antechamber to
> generate the parameter file for graphene oxide.Pls help me
> Info: the bond number exceeds MAXBOND, reallocate memory automatically
>
> Info: the bond number exceeds the MAXBOND, reallocate memory, automatically
> Info: the actual number of rings (7134) exceeds the defaut ring size
> (500), reallocate memory automatically
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase PSCUTOFF in define.h and recompile bondtype.c
>     Be cautious, use a large value of PSCUTOFF (>100) will
> significantly increase the computation time
>
> Info: the bond number exceeds the MAXBOND, reallocate memory, automatically
> Info: the actual number of rings (7134) exceeds the defaut ring size
> (500), reallocate memory automaticallyTotal number of electrons: 3931;
> net charge: 1
> INFO: Number of electrons is odd: 3931
>       Please check the total charge (-nc flag) and spin multiplicity (-m
> flag)
>
> Running: /home/pinak/amber14/bin/sqm -O -i sqm.in -o sqm.out
> Error: cannot run "/home/pinak/amber14/bin/sqm -O -i sqm.in -o
> sqm.out" of bcc() in charge.c properly, exit
>
> On Tue, Feb 23, 2016 at 5:04 PM, Jesmita Dhar <dhar.beauty.gmail.com>
> wrote:
> > Dear sir/madam,
> >                          I have docked graphene oxide to human
> > lysozyme protein. I want to run md simulation, but can not able
> > generate the parameter file using antechamber as its very large
> > sturcture.
>
>
>
> ------------------------------
>
> Message: 11
> Date: Thu, 25 Feb 2016 10:54:23 +0100
> From: Karl Kirschner <k.n.kirschner.gmail.com>
> Subject: Re: [AMBER] parameter file for graphene oxide
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
>         <CAF=
> D-bwjZqszvYfSPe4w68QxQ4AdMwyJKF4JSOHuuEueHQFWFg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hello Jesmita,
>
>   It appears that your molecule is very very big. Try using a smaller
> analogue of your larger graphene oxide sheet - one that captures the unique
> chemical functionalities (e.g. bonds, angle and torsions). Run this smaller
> analogue into antechamber to get some suggestions for parameters. If you
> have correctly accounted for all of the unique internal coordinates in your
> analogue, then the resulting parameters "should" be transferable to the
> larger sheet. The one thing that might need some additional consideration
> is the partial atomic charges, and if your analogue captures the
> delocalization that is present in the larger sheet.
>
> Bests,
> Karl
>
> On Thu, Feb 25, 2016 at 10:36 AM, Jesmita Dhar <dhar.beauty.gmail.com>
> wrote:
>
> > Hello,
> > We are getting the following error while we have run antechamber to
> > generate the parameter file for graphene oxide.Pls help me
> > Info: the bond number exceeds MAXBOND, reallocate memory automatically
> >
> > Info: the bond number exceeds the MAXBOND, reallocate memory,
> automatically
> > Info: the actual number of rings (7134) exceeds the defaut ring size
> > (500), reallocate memory automatically
> > Warning: the assigned bond types may be wrong, please :
> > (1) double check the structure (the connectivity) and/or
> > (2) adjust atom valence penalty parameters in APS.DAT, and/or
> > (3) increase PSCUTOFF in define.h and recompile bondtype.c
> >     Be cautious, use a large value of PSCUTOFF (>100) will
> > significantly increase the computation time
> >
> > Info: the bond number exceeds the MAXBOND, reallocate memory,
> automatically
> > Info: the actual number of rings (7134) exceeds the defaut ring size
> > (500), reallocate memory automaticallyTotal number of electrons: 3931;
> > net charge: 1
> > INFO: Number of electrons is odd: 3931
> >       Please check the total charge (-nc flag) and spin multiplicity (-m
> > flag)
> >
> > Running: /home/pinak/amber14/bin/sqm -O -i sqm.in -o sqm.out
> > Error: cannot run "/home/pinak/amber14/bin/sqm -O -i sqm.in -o
> > sqm.out" of bcc() in charge.c properly, exit
> >
> > On Tue, Feb 23, 2016 at 5:04 PM, Jesmita Dhar <dhar.beauty.gmail.com>
> > wrote:
> > > Dear sir/madam,
> > >                          I have docked graphene oxide to human
> > > lysozyme protein. I want to run md simulation, but can not able
> > > generate the parameter file using antechamber as its very large
> > > sturcture.
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Karl. N. Kirschner, Ph.D.
> Research Associate
> Bonn-Rhein-Sieg University of Applied Sciences
> Grantham-Allee 20, 54757 Sankt Augustin, Germany
>
>
> ------------------------------
>
> Message: 12
> Date: Thu, 25 Feb 2016 10:17:15 +0000
> From: Anna Cebrian Prats <Anna.Cebrian.uab.cat>
> Subject: [AMBER] Minimization error using Sander
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID:
>         <
> DBXPR07MB461904604177B69FBFA13A88AA60.DBXPR07MB461.eurprd07.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I am trying to run the minimization with sander
> using a .top file and the inpcrd file as a result of
> using the chamber (executable that convert charmm files to amber files)
> of amber14. The system constitute a large protein with a Fe+2 coordinated
> with
> 5 residues and a "-OH"
>
> The problem is that I obtain the follow message:
>
>
>
> --------------------------------------------------------------------------------
>
> 4. RESULTS
>
>
> --------------------------------------------------------------------------------
>
> ---------------------------------------------------
>
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
>
> using 5000.0 points per unit in tabled values
>
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
>
> | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
>
> ---------------------------------------------------
>
> * NB pairs 1726 52366155 exceeds capacity ( 52366666)
>
> SIZE OF NONBOND LIST = 52366666
>
> SANDER BOMB in subroutine nonbond_list
>
> Non bond list overflow!
>
> check MAXPR in locmem.f
>
>
> I already check MAXPR of the locmen.f and try to modify the assignment
> to maxpr_float two the lines below:
>
>
> >> maxpr_float = natom * (cutoffnb + skinnb)**3 / 2.5d0
>
> >> to
>
> >> maxpr_float = natom * (cutoffnb + skinnb)**3 / 1.5d0
>
>
> and still not working.
>
>
> May I use the pmemd.mpi ? or what I have to check to solve the error?
>
>
> Thank you
>
> Anna
>
>
>
> ------------------------------
>
> Message: 13
> Date: Thu, 25 Feb 2016 03:27:55 -0800
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] Minimization error using Sander
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <56CEE53B.20804.cgl.ucsf.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>  > * NB pairs 1726 52366155 exceeds capacity ( 52366666)
>
> It is interesting that there are two numbers printed for NB pairs, 1726
> and 52366155.
>
> You might try
>
> % grep 'exceeds capacity' *.f
>
> to find where the error is coming from and which variables are
> triggering it. I don't have the source these days. It may be something
> other than maxpr_float.
>
> Bill
>
>
> On 2/25/16 2:17 AM, Anna Cebrian Prats wrote:
> > Hi,
> >
> > I am trying to run the minimization with sander
> > using a .top file and the inpcrd file as a result of
> > using the chamber (executable that convert charmm files to amber files)
> > of amber14. The system constitute a large protein with a Fe+2
> coordinated with
> > 5 residues and a "-OH"
> >
> > The problem is that I obtain the follow message:
> >
> >
> >
> --------------------------------------------------------------------------------
> >
> > 4. RESULTS
> >
> >
> --------------------------------------------------------------------------------
> >
> > ---------------------------------------------------
> >
> > APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> >
> > using 5000.0 points per unit in tabled values
> >
> > TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> >
> > | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> >
> > | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
> >
> > ---------------------------------------------------
> >
> > * NB pairs 1726 52366155 exceeds capacity ( 52366666)
> >
> > SIZE OF NONBOND LIST = 52366666
> >
> > SANDER BOMB in subroutine nonbond_list
> >
> > Non bond list overflow!
> >
> > check MAXPR in locmem.f
> >
> >
> > I already check MAXPR of the locmen.f and try to modify the assignment
> > to maxpr_float two the lines below:
> >
> >
> >>> maxpr_float = natom * (cutoffnb + skinnb)**3 / 2.5d0
> >>> to
> >>> maxpr_float = natom * (cutoffnb + skinnb)**3 / 1.5d0
> >
> > and still not working.
> >
> >
> > May I use the pmemd.mpi ? or what I have to check to solve the error?
> >
> >
> > Thank you
> >
> > Anna
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 14
> Date: Thu, 25 Feb 2016 08:16:49 -0500
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Minimization error using Sander
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20160225131649.GD62981.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Thu, Feb 25, 2016, Anna Cebrian Prats wrote:
> >
> > I am trying to run the minimization with sander
> > using a .top file and the inpcrd file as a result of
> > using the chamber (executable that convert charmm files to amber files)
> > of amber14. The system constitute a large protein with a Fe+2
> coordinated with
> > 5 residues and a "-OH"
> >
> > * NB pairs 1726 52366155 exceeds capacity ( 52366666)
>
> How many atoms are in your system.  What value of cut did you give in the
> input file?  (Try the default value if you are using a bigger value now.)
>
> You can certainly try pmemd.  Don't do anything in parallel until you can
> get
> the system working correctly in serial mode.
>
> > I already check MAXPR of the locmen.f and try to modify the assignment
> > to maxpr_float two the lines below:
> >
> > >> maxpr_float = natom * (cutoffnb + skinnb)**3 / 2.5d0
> > >> to
> > >> maxpr_float = natom * (cutoffnb + skinnb)**3 / 1.5d0
>
> Just to be sure: did you re-compile after making this change?
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 15
> Date: Thu, 25 Feb 2016 13:25:55 +0000
> From: BLEY Michael <Michael.BLEY.cea.fr>
> Subject: [AMBER] Maximum input value for the isothermal
>         compressibility in      AMBER
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID:
>         <40120A1BD1312E45BB862454C7D74018BBDF69.EXDAG0-B2.intra.cea.fr>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
> Hello,
>
> I just started a project on determining the equation of state for both
> liquid and gaseous water by molecular dynamics with the POL3 water model.
> For the liquid state it was obviously no big deal to determine the relation
> between pressure and density at room temperature, but for the gaseous state
> I have some problems with the upper limit of the isothermal compressibility
> in AMBER. The highest value which seem to be accepted as valid input is
> 9.999 * 10^-3 bar^-1.
> Is it somehow possible to use higher values for the COMP-input parameter
> in AMBER or is there no limitation for this value at all?
> It is the first time that I am using the AMBER mailing list, so let me
> please know if some important or data is missing. Thank you very much for
> your efforts.
>
> Sincerely yours,
>
> Michael Bley
>
> ----------------------
> michael.bley.cea.fr
> PhD student
> ICSM Marcoule
> LMCT Group
>
>
> ------------------------------
>
> Message: 16
> Date: Thu, 25 Feb 2016 09:06:39 -0500
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Maximum input value for the isothermal
>         compressibility in AMBER
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20160225140639.GA63226.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Thu, Feb 25, 2016, BLEY Michael wrote:
> >
> > I just started a project on determining the equation of state for both
> > liquid and gaseous water by molecular dynamics with the POL3 water
> > model. For the liquid state it was obviously no big deal to determine
> > the relation between pressure and density at room temperature, but for
> > the gaseous state I have some problems with the upper limit of the
> > isothermal compressibility in AMBER. The highest value which seem to be
> > accepted as valid input is 9.999 * 10^-3 bar^-1.
> > Is it somehow possible to use higher values for the COMP-input parameter
> > in AMBER or is there no limitation for this value at all?
> > It is the first time that I am using the AMBER mailing list, so let me
> > please know if some important or data is missing. Thank you very much
> > for your efforts.
>
> The value of compressibility is only used as a way to convert units in
> the Berendsen barostat: it is not related in any real way to isothermal
> compressibility.  So (in principle) you can just use the default (liquid)
> value.
>
> Having said that, I'm not sure you can effectively use Amber to look at
> non-ideal gases (but it might be fun to try!).  Maintaining the desired
> temperature and pressure is tricky in a gas.  I think you would have to
> use a Langevin thermostat and the Monte Carlo barostat, and be prepared
> for lots of experimentation.  Your density will be a thousand times
> smaller than what the code was designed for, so there may be lots of
> hidden gotchas.  I'd certainly recommend starting with a simpler water
> model (such as TIP3P) first, just to reduce the number of sources of
> error.
>
> My guess is that at best, you will get back the ideal gas limit for the
> equation of state, but I might be wrong.  Sounds like an interesting
> educational exercise.  Maybe someone else on the list has actually tried
> this
> and can chime in here.
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 17
> Date: Thu, 25 Feb 2016 14:24:54 +0000
> From: Anna Cebrian Prats <Anna.Cebrian.uab.cat>
> Subject: Re: [AMBER] Minimization error using Sander
> To: AMBER Mailing List <amber.ambermd.org>, "david.case.rutgers.edu"
>         <david.case.rutgers.edu>
> Message-ID:
>         <
> DBXPR07MB461C1BA2FE93EE17098E0F38AA60.DBXPR07MB461.eurprd07.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you to answer.
>
> The system have 10750 atoms including the Fe+2.
> The cutoff that I used is the default one, cut=8.0 with igb=0.
>
> Respect to the changes, I recompiled when I made the changes.
>
> But, following jaime 's answer, I already visualize the pdb file with the
> prmtop obtained using chamber ( that convert the charmm files to the amber
> files), and the protein don't have connectivity all the atoms appear with
> any bond connection, so as individual atoms.
>
> Then the problem is with chamber. Then I don't know how to solve it, due
> to I use the typical usage of the manual amber14.
>
> Anna
>
> ________________________________________
> De: David A Case <david.case.rutgers.edu>
> Enviat el: dijous, 25 de febrer de 2016 14:16
> Per a: AMBER Mailing List
> Tema: Re: [AMBER] Minimization error using Sander
>
> On Thu, Feb 25, 2016, Anna Cebrian Prats wrote:
> >
> > I am trying to run the minimization with sander
> > using a .top file and the inpcrd file as a result of
> > using the chamber (executable that convert charmm files to amber files)
> > of amber14. The system constitute a large protein with a Fe+2
> coordinated with
> > 5 residues and a "-OH"
> >
> > * NB pairs 1726 52366155 exceeds capacity ( 52366666)
>
> How many atoms are in your system.  What value of cut did you give in the
> input file?  (Try the default value if you are using a bigger value now.)
>
> You can certainly try pmemd.  Don't do anything in parallel until you can
> get
> the system working correctly in serial mode.
>
> > I already check MAXPR of the locmen.f and try to modify the assignment
> > to maxpr_float two the lines below:
> >
> > >> maxpr_float = natom * (cutoffnb + skinnb)**3 / 2.5d0
> > >> to
> > >> maxpr_float = natom * (cutoffnb + skinnb)**3 / 1.5d0
>
> Just to be sure: did you re-compile after making this change?
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 18
> Date: Thu, 25 Feb 2016 14:25:54 +0000
> From: Mahdieh Hadi <mahdieh.hadi.bric.ku.dk>
> Subject: [AMBER] Question regarding protein-Dna binding free energy
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID:
>
> <D3E31A7831C8194688C4791851B9D1800E302862.P2KITMBX02WC01.unicph.domain>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
> I have prepared pdb, inpcrd and prompt files for my DNA, and I have pdb
> file of my protein. But I do not have the complex of them. I am going to
> predict the mutations in my DNA sequence that will decrease the binding
> affinity to the protein to the least level.
> Would you please give me an overview of what should I do? How should I
> prepare DNA-Protein complex and etc?
> Bests
> Mahdieh
>
>
> ------------------------------
>
> Message: 19
> Date: Thu, 25 Feb 2016 15:52:15 +0100
> From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
> Subject: Re: [AMBER] Question regarding protein-Dna binding free
>         energy
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <56CF151F.5020509.mpi-muenster.mpg.de>
> Content-Type: text/plain; charset="windows-1252"; format=flowed
>
> Well, you are asking for different entire training sessions by email ...
> I guess you realize this is not really possible. Maybe you could start
> in searching the literature about how to predict the configuration of
> protein-DNA complexes when you don't know the structure (a research
> topic on its own)  ... Once you have a complex and you are confident in
> it (validation very important), you may attempt rough predictions of
> base-dependent differences in DNA binding affinity (another research
> topic on its own, Rosetta software may be an interesting starting point
> ) ..  Or you may want to simulate it with classical MD or advanced
> enhanced sampling techniques (other research topics on their own)...
>
> So, probably what you have to do is to read and read and read before you
> can start something ....
>
> Vlad
>
>
> On 02/25/2016 03:25 PM, Mahdieh Hadi wrote:
> > Hi,
> > I have prepared pdb, inpcrd and prompt files for my DNA, and I have pdb
> file of my protein. But I do not have the complex of them. I am going to
> predict the mutations in my DNA sequence that will decrease the binding
> affinity to the protein to the least level.
> > Would you please give me an overview of what should I do? How should I
> prepare DNA-Protein complex and etc?
> > Bests
> > Mahdieh
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> R?ntgenstrasse 20, 48149 M?nster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
>
>
> ------------------------------
>
> Message: 20
> Date: Thu, 25 Feb 2016 14:56:48 +0000
> From: Mahdieh Hadi <mahdieh.hadi.bric.ku.dk>
> Subject: Re: [AMBER] Question regarding protein-Dna binding free
>         energy
> To: AMBER Mailing List <amber.ambermd.org>, Vlad Cojocaru
>         <vlad.cojocaru.mpi-muenster.mpg.de>
> Message-ID:
>
> <D3E31A7831C8194688C4791851B9D1800E3028E7.P2KITMBX02WC01.unicph.domain>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thanks a lot for your answer. :)
> So, I just use amber for investigating interactions between DNA and
> Protein, if I have their complex. Is it true?
> And superimposition of them is not possible by Amber. Yes?
>
> ________________________________________
> From: Vlad Cojocaru [vlad.cojocaru.mpi-muenster.mpg.de]
> Sent: Thursday, February 25, 2016 3:52 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Question regarding protein-Dna binding free energy
>
> Well, you are asking for different entire training sessions by email ...
> I guess you realize this is not really possible. Maybe you could start
> in searching the literature about how to predict the configuration of
> protein-DNA complexes when you don't know the structure (a research
> topic on its own)  ... Once you have a complex and you are confident in
> it (validation very important), you may attempt rough predictions of
> base-dependent differences in DNA binding affinity (another research
> topic on its own, Rosetta software may be an interesting starting point
> ) ..  Or you may want to simulate it with classical MD or advanced
> enhanced sampling techniques (other research topics on their own)...
>
> So, probably what you have to do is to read and read and read before you
> can start something ....
>
> Vlad
>
>
> On 02/25/2016 03:25 PM, Mahdieh Hadi wrote:
> > Hi,
> > I have prepared pdb, inpcrd and prompt files for my DNA, and I have pdb
> file of my protein. But I do not have the complex of them. I am going to
> predict the mutations in my DNA sequence that will decrease the binding
> affinity to the protein to the least level.
> > Would you please give me an overview of what should I do? How should I
> prepare DNA-Protein complex and etc?
> > Bests
> > Mahdieh
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> R?ntgenstrasse 20, 48149 M?nster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 21
> Date: Thu, 25 Feb 2016 16:15:32 +0100
> From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
> Subject: Re: [AMBER] Question regarding protein-Dna binding free
>         energy
> To: Mahdieh Hadi <mahdieh.hadi.bric.ku.dk>
> Cc: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <56CF1A94.2080706.mpi-muenster.mpg.de>
> Content-Type: text/plain; charset="windows-1252"; format=flowed
>
> Sure ... If you start searching for protein-DNA docking procedures you
> should some way to start ...
> You could maybe start with this recent paper ... References in the paper
> should also be useful
>
> http://nar.oxfordjournals.org/content/early/2015/05/14/nar.gkv493.full
>
> Ideally you would use different docking methods and come to the same
> result ... Plus validation (ideally some sort experimental validation)
> may be needed ....
>
> But again, the situation changes and becomes significantly more easy if
> your protein has a known type of fold for which structures of complexes
> with DNA exist ...
>
> Best
> Vlad
>
>
> On 02/25/2016 04:08 PM, Mahdieh Hadi wrote:
> > I have a dna sequence and my protein structure. I do not have the
> complex structure of them. And I am going to investigate the binding energy
> between non mutated Dna and protein. Then I am going to do the same for Dna
> sequence with different mutations to find the mutations which will destroy
> the interactions completely.
> > But, I think that a low quality docking will destroy all of my
> predictions and at first I should find the best approach for docking.
> > Bests!
> > ________________________________________
> > From: Vlad Cojocaru [vlad.cojocaru.mpi-muenster.mpg.de]
> > Sent: Thursday, February 25, 2016 4:04 PM
> > To: Mahdieh Hadi
> > Subject: Re: [AMBER] Question regarding protein-Dna binding free energy
> >
> > Well. what do you mean by superposition  ?? As far I understand your
> > question, you actually need to dock them first, validate your results
> > from the docking before you can say you have a reliable complex
> > structure. Of course if protein has homologs for which a structure with
> > DNA is available, homology modeling may be enough ....   Hard to say
> > what you actually need from your description ...
> >
> > Vlad
> >
> > On 02/25/2016 03:56 PM, Mahdieh Hadi wrote:
> >> Thanks a lot for your answer. :)
> >> So, I just use amber for investigating interactions between DNA and
> Protein, if I have their complex. Is it true?
> >> And superimposition of them is not possible by Amber. Yes?
> >>
> >> ________________________________________
> >> From: Vlad Cojocaru [vlad.cojocaru.mpi-muenster.mpg.de]
> >> Sent: Thursday, February 25, 2016 3:52 PM
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] Question regarding protein-Dna binding free energy
> >>
> >> Well, you are asking for different entire training sessions by email ...
> >> I guess you realize this is not really possible. Maybe you could start
> >> in searching the literature about how to predict the configuration of
> >> protein-DNA complexes when you don't know the structure (a research
> >> topic on its own)  ... Once you have a complex and you are confident in
> >> it (validation very important), you may attempt rough predictions of
> >> base-dependent differences in DNA binding affinity (another research
> >> topic on its own, Rosetta software may be an interesting starting point
> >> ) ..  Or you may want to simulate it with classical MD or advanced
> >> enhanced sampling techniques (other research topics on their own)...
> >>
> >> So, probably what you have to do is to read and read and read before you
> >> can start something ....
> >>
> >> Vlad
> >>
> >>
> >> On 02/25/2016 03:25 PM, Mahdieh Hadi wrote:
> >>> Hi,
> >>> I have prepared pdb, inpcrd and prompt files for my DNA, and I have
> pdb file of my protein. But I do not have the complex of them. I am going
> to predict the mutations in my DNA sequence that will decrease the binding
> affinity to the protein to the least level.
> >>> Would you please give me an overview of what should I do? How should I
> prepare DNA-Protein complex and etc?
> >>> Bests
> >>> Mahdieh
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >> --
> >> Dr. Vlad Cojocaru
> >> Computational Structural Biology Laboratory
> >> Department of Cell and Developmental Biology
> >> Max Planck Institute for Molecular Biomedicine
> >> R?ntgenstrasse 20, 48149 M?nster, Germany
> >> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> >> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> >> http://www.mpi-muenster.mpg.de/43241/cojocaru
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > --
> > Dr. Vlad Cojocaru
> > Computational Structural Biology Laboratory
> > Department of Cell and Developmental Biology
> > Max Planck Institute for Molecular Biomedicine
> > R?ntgenstrasse 20, 48149 M?nster, Germany
> > Tel: +49-251-70365-324; Fax: +49-251-70365-399
> > Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> > http://www.mpi-muenster.mpg.de/43241/cojocaru
> >
>
> --
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> R?ntgenstrasse 20, 48149 M?nster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
>
>
> ------------------------------
>
> Message: 22
> Date: Thu, 25 Feb 2016 18:24:38 +0100
> From: Indrajit Deb <biky2004indra.gmail.com>
> Subject: [AMBER] MMGBSA error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
>         <
> CAKg8EVZmx1Ef3j9YHQNxuSCFo2mkvGcUR6LYRX_vXw1WyYQ3Cg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Users,
>
> I am trying to carryout MMPBSA calculations in serial with AMBER14 and
> AMBERTOOLS15 with latest updates. Everything (GB, PB, Quasi harmonic and
> Normal mode) is working fine for my control RNA duplex and also for one
> mutated duplex. But for another mutated duplex I am getting the following
> error....
>
>
> Running calculations on normal system...
>
> Beginning GB calculations with
> /home/indra/amber14-tools15/amber14/bin/mmpbsa_py_energy
>   calculating complex contribution...
> bad value for Pn: 393 396 411 414    7.000
>   File "/home/indra/amber14-tools15/amber14/bin/MMPBSA.py", line 104, in
> <module>
>     app.run_mmpbsa()
>   File
>
> "/home/indra/amber14-tools15/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
>     self.calc_list.run(rank, self.stdout)
>   File
>
> "/home/indra/amber14-tools15/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
>     calc.run(rank, stdout=stdout, stderr=stderr)
>   File
>
> "/home/indra/amber14-tools15/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 157, in run
>     self.prmtop))
> CalcError: /home/indra/amber14-tools15/amber14/bin/mmpbsa_py_energy failed
> with prmtop dry-complex.prmtop!
> Exiting. All files have been retained.
>
> ?If anyone have any idea, please help.
>
> Thanks
>
> ----indrajit
>
>
>
> --------------------------------------------------------------------------------------------------------------
> *Indrajit Deb*
> alternate emails: indrajitdeb81.gmail.com, idbmbg_s.caluniv.ac.in
> *Present Position*
> International Centre for Genetic Engineering and Biotechnology (ICGEB,
> Italy) SMART Fellow,
> Department of Structural Chemistry and Biology of Nucleic Acids,
> Institute of Bioorganic Chemistry (IBCh),
> Polish Academy of Sciences (PAS).
> European Center for Bioinformatiocs and Genetics (ECBiG) Campus (
> R
> oom: 2.6.28
> ).
> Z. Noskowskiego Str. 12/14.
> Poznan 61-704, Poland?.
> Phone: +48616653042, ?Personal Mobile: +48662513522?
> ?
> *Previous Position*?
> Ph.D Student,
> Department of Biophysics, Molecular Biology and Bioinformatics, University
> of Calcutta (CU), 92 APC Road, Kolkata - 700009, India. Phone:
> +913323508386 (extn. 329, 321), Fax: +913323519755. Personal Mobile:
> +919239202278
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 1497, Issue 1
> **************************************
>
-- 
Necmettin Pirinccioglu (BSc, PhD)
Department of Chemistry
University of Dicle
21280 Diyarbakir
TURKEY



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Received on Fri Feb 26 2016 - 05:30:04 PST
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