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-- 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