Hi,
Did you follow all of the advice that Ross gave you? In particular,
SHAKE errors usually stem from inadequate minimization. What was your
minimization/equilibration protocol? You may need to extend it.
-Dan
On Fri, Feb 26, 2016 at 6:21 AM, 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
>
>
> ------------------------------
>
> 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:
>
>> Send AMBER mailing list submissions to
>> amber.ambermd.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://lists.ambermd.org/mailman/listinfo/amber
>> or, via email, send a message with subject or body 'help' to
>> amber-request.ambermd.org
>>
>> You can reach the person managing the list at
>> amber-owner.ambermd.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of AMBER digest..."
>>
>>
>> AMBER Mailing List Digest
>>
>> Today's Topics:
>>
>> 1. Re: 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
>> Size: 38170 bytes
>> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 26 2016 - 07:30:09 PST
