Just for completeness: GLYCAM06 is much better than GLYCAM04...
On Tue, Sep 20, 2016 at 4:57 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Yuan,
>
> this is the FF version from the amber10 distribution; I am going to
> add it in the F-85 REDDB project;
> this will be done by tomorrow...
> See http://upjv.q4md-forcefieldtools.org/REDDB/projects/F-85/
> i.e. in place of
> http://upjv.q4md-forcefieldtools.org/REDDB/projects/F-85/script5.ff
>
> regards, Francois
>
>
> Quoting Helen Lvy <helenyuan0302.outlook.com>:
>
> > Dear Francois,
> >
> >
> > I saw a mail about q4md-CD FF and Glycam04 FF, may I know which
> > Glycam04 file you use for q4md-CD FF? Thank you very much. Part of
> > the mail is attached below:
> >
> >
> >> I am using Amber12, which did not include Glycam04, There are
> >> Glycam04_a,Glycam04_b ...... Glycam04_k, Glycam04_l in official website,
> >> http://glycam.ccrc.uga.edu/ccrc/pages/parameters.html, which one
> >> should I download?
> >
> > I have no idea: I cannot understand this classification.
> > I will send to your private email the Glycam04 file we used...
> >
> >
> > Sincerely
> >
> > Yuan
> >
> >
> >
> >
> > ________________________________
> > From: amber-request.ambermd.org <amber-request.ambermd.org>
> > Sent: Wednesday, September 14, 2016 3:00 PM
> > To: amber.ambermd.org
> > Subject: AMBER Digest, Vol 1697, Issue 1
> >
> > 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
> > AMBER -- AMBER Mailing List<http://lists.ambermd.org/
> mailman/listinfo/amber>
> > lists.ambermd.org
> > AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing
> > List. It is designed to provide a forum for users of the AMBER
> > Molecular Dynamics and related ...
> >
> >
> >
> > 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. FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type.
> > Failed to generate parameters Parameter file was not saved.
> > (shahab shariati)
> > 2. MM-PBSA, Protein-nucleic acids free energy calculations
> > (hari krishna)
> > 3. Fwd: query with amber (Pooja Kesari)
> > 4. Re: FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type.
> > Failed to generate parameters Parameter file was not saved.
> > (Bill Ross)
> > 5. Re: Fwd: query with amber (Bill Ross)
> > 6. Re: Fwd: query with amber (Pooja Kesari)
> > 7. Re: Fwd: query with amber (Bill Ross)
> > 8. Re: MM-PBSA, Protein-nucleic acids free energy calculations
> > (Carlos Simmerling)
> > 9. How to "not" strip an ion (say Mg) in MMPBSA (Hirdesh Kumar)
> > 10. Force field ff14SB (Anna Cebrian Prats)
> > 11. Re: Fullerene RESP charges derivation (David A Case)
> > 12. Re: FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type.
> > Failed to generate parameters Parameter file was not saved.
> > (David A Case)
> > 13. Re: MM-PBSA, Protein-nucleic acids free energy calculations
> > (David A Case)
> > 14. Re: Fwd: query with amber (David A Case)
> > 15. R: Fullerene RESP charges derivation (Fabio Bologna)
> > 16. Parameters for GppNHp ligand. (Dd H)
> > 17. Re: MM-PBSA, Protein-nucleic acids free energy calculations
> > (Vlad Cojocaru)
> > 18. Re: How to "not" strip an ion (say Mg) in MMPBSA (Bruno Falcone)
> > 19. Re: How to "not" strip an ion (say Mg) in MMPBSA (Jason Swails)
> > 20. Re: Force field ff14SB (Jason Swails)
> > 21. Re: Force field ff14SB (Carlos Simmerling)
> > 22. Re: Force field ff14SB (Anna Cebrian Prats)
> > 23. Re: MM-PBSA, Protein-nucleic acids free energy calculations
> > (hari krishna)
> > 24. Re: MM-PBSA, Protein-nucleic acids free energy calculations
> > (Jiri Sponer)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 14 Sep 2016 09:59:57 +0430
> > From: shahab shariati <shahab.shariati.gmail.com>
> > Subject: [AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a
> > type. Failed to generate parameters Parameter file was not saved.
> > To: amber <amber.ambermd.org>
> > Message-ID:
> > <CANW_mVvrDJs37w+Wt9wwH5bbnT_wPcx6Z5jCC=sNAp+vHPYUdA.mail.
> gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Dear Samuel,
> >
> > Thanks for your answer. My previous problem (cannot run
> > "/share/apps/amber/amber14/bin/sqm
> > -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit) was
> solved.
> >
> > Now, I have another problem. For my protein structure, I used following
> > commands:
> >
> > $AMBERHOME/exe/reduce pr_h.pdb > pr.pdb
> >
> > tleap -f pr.in
> >
> > pr.in file is as follows:
> >
> > source leaprc.ff99SB
> >
> > pr = loadpdb pr.pdb
> >
> > set default PBRadii mbondi2
> >
> > saveamberparm pr pr.prmtop pr.inpcrd
> >
> > quit
> >
> > ---------------------------------------------------------
> > But, I encountered with:
> >
> > FATAL: Atom .R<CLEU 124>.A<H04 25> does not have a type.
> > FATAL: Atom .R<CLEU 124>.A<H05 26> does not have a type.
> > FATAL: Atom .R<CLEU 124>.A<H06 27> does not have a type.
> > FATAL: Atom .R<CLEU 124>.A<H07 28> does not have a type.
> > FATAL: Atom .R<CLEU 124>.A<H08 29> does not have a type.
> > FATAL: Atom .R<CLEU 124>.A<H09 30> does not have a type.
> > FATAL: Atom .R<CLEU 124>.A<H10 31> does not have a type.
> > FATAL: Atom .R<CLEU 124>.A<H11 32> does not have a type.
> > FATAL: Atom .R<CLEU 124>.A<H12 33> does not have a type.
> > FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type.
> > Failed to generate parameters
> > Parameter file was not saved.
> >
> > There is this error for most of the Hydrogen atoms.
> >
> > How to resolve this problem?
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Wed, 14 Sep 2016 11:00:10 +0530
> > From: hari krishna <haricoolguy111.gmail.com>
> > Subject: [AMBER] MM-PBSA, Protein-nucleic acids free energy
> > calculations
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <CADa8WMrMy87QLDYP8AXbjSyjA4LcGfhAbgdEsBTDnGXxsj+EPw.mail.
> gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi all,
> >
> > We have carried microsecond simulations for a protein (800 aa) - RNA (17
> > bp) systems. Various modified RNA molecules have been used to find the
> > binding specificity/affinity with the same protein. The free energy of
> > binding was calculated using MM-PBSA method. The entropic contribution
> was
> > calculated using NMODE method. The free energy values (dG) are in the
> > range of -250 kcal/mol. However, among the various systems used, the
> > difference in the free energy values(ddG) are in the range of 10 to 30
> > kcal/mol. These numbers are more or less to similar to the standard
> > deviation of the free energy obtained MM-PBSA calculations. Are these
> > error values obtained from the calculations quantitatively correct? Is it
> > safe to report such free energy changes in publications. If not, is there
> > any other better way to calculate the absolute free energy other than
> > approximation methods using AMBER package?
> >
> > Harikrishna
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Wed, 14 Sep 2016 11:30:50 +0530
> > From: Pooja Kesari <pkesari88.gmail.com>
> > Subject: [AMBER] Fwd: query with amber
> > To: amber.ambermd.org
> > Message-ID:
> > <CAH1aNEAvuqPHKRXGqYK2G8A8YKDqE6s_qKJu4RwfqNP1C_pRwQ.mail.
> gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear All,
> > I have a query regarding amber installation
> > My amber folder is located in
> > /usr/bin/amber11/
> >
> > in my tcshrc file i have defined the path
> >
> > setenv AMBERHOME "/usr/local/amber11"
> > set PATH=($path $AMBERHOME)
> > setenv LD_LIBRARY_PATH "/usr/lib64/openmpi/lib"
> > set path = ($path $LD_LIBRARY_PATH)
> >
> > 1. now if i run a job it says
> > *mpirun -np 60 sander.MPI -O -i prod.in <http://prod.in> -o
> > prod_complex-solv.out -p complex-solv.prmtop -c protein_solv-equil.rst -r
> > protein_solv-prod.rst -x prod.mdcrd -ref protein_solv-equil.rst *
> > ------------------------------------------------------------
> --------------
> > mpirun was unable to launch the specified application as it could not
> find
> > an executable:
> > Executable: sander.MPI
> > while attempting to start process rank 0.
> >
> > 2. If i defined the path of sander mpi it says
> > *mpirun -np 60 /usr/local/amber11/bin/sander.MPI -O -i prod.in
> > <http://prod.in> -o prod_complex-solv.out -p complex-solv.prmtop -c
> > protein_solv-equil.rst -r protein_solv-prod.rst -x prod.mdcrd -ref
> > protein_solv-equil.rst *
> > /usr/local/amber11/bin/sander.MPI: error while loading shared libraries:
> > libmpi_f90.so.0: cannot open shared object file: No such file or
> directory
> > /usr/local/amber11/bin/sander.MPI: error while loading shared libraries:
> > libmpi_f90.so.0: cannot open shared object file: No such file or
> directory
> > /usr/local/amber11/bin/sander.MPI: error while loading shared libraries:
> > libmpi_f90.so.0: cannot open shared object file: No such file or
> directory
> > /usr/local/amber11/bin/sander.MPI: error while loading shared libraries:
> > libmpi_f90.so.0: cannot open shared object file: No such file or
> directory
> > /usr/local/amber11/bin/sander.MPI: error while loading shared libraries:
> > libmpi_f90.so.0: cannot open shared object file: No such file or
> directory
> >
> > Please help
> >
> > --
> > Thanks & Regards,
> > Pooja Kesari
> > -------------- next part --------------
> > A non-text attachment was scrubbed...
> > Name: Screenshot.png
> > Type: image/png
> > Size: 390799 bytes
> > Desc: not available
> > Url :
> > http://lists.ambermd.org/mailman/private/amber/
> attachments/20160914/6f039f2f/attachment-0001.png
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Tue, 13 Sep 2016 23:32:36 -0700
> > From: Bill Ross <ross.cgl.ucsf.edu>
> > Subject: Re: [AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have
> > a type. Failed to generate parameters Parameter file was not
> saved.
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID: <a07b115c-42d8-5d26-b595-8ae0db12548b.cgl.ucsf.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > I suspect there were messages about missing and extra atoms for loadpdb,
> > and that adding these up would lead to the conclusion that your H atoms
> > are misnamed in the pdb.
> >
> > Bill
> >
> >
> > On 9/13/16 10:29 PM, shahab shariati wrote:
> >> Dear Samuel,
> >>
> >> Thanks for your answer. My previous problem (cannot run
> >> "/share/apps/amber/amber14/bin/sqm
> >> -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit) was
> solved.
> >>
> >> Now, I have another problem. For my protein structure, I used following
> >> commands:
> >>
> >> $AMBERHOME/exe/reduce pr_h.pdb > pr.pdb
> >>
> >> tleap -f pr.in
> >>
> >> pr.in file is as follows:
> >>
> >> source leaprc.ff99SB
> >>
> >> pr = loadpdb pr.pdb
> >>
> >> set default PBRadii mbondi2
> >>
> >> saveamberparm pr pr.prmtop pr.inpcrd
> >>
> >> quit
> >>
> >> ---------------------------------------------------------
> >> But, I encountered with:
> >>
> >> FATAL: Atom .R<CLEU 124>.A<H04 25> does not have a type.
> >> FATAL: Atom .R<CLEU 124>.A<H05 26> does not have a type.
> >> FATAL: Atom .R<CLEU 124>.A<H06 27> does not have a type.
> >> FATAL: Atom .R<CLEU 124>.A<H07 28> does not have a type.
> >> FATAL: Atom .R<CLEU 124>.A<H08 29> does not have a type.
> >> FATAL: Atom .R<CLEU 124>.A<H09 30> does not have a type.
> >> FATAL: Atom .R<CLEU 124>.A<H10 31> does not have a type.
> >> FATAL: Atom .R<CLEU 124>.A<H11 32> does not have a type.
> >> FATAL: Atom .R<CLEU 124>.A<H12 33> does not have a type.
> >> FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type.
> >> Failed to generate parameters
> >> Parameter file was not saved.
> >>
> >> There is this error for most of the Hydrogen atoms.
> >>
> >> How to resolve this problem?
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Tue, 13 Sep 2016 23:39:41 -0700
> > From: Bill Ross <ross.cgl.ucsf.edu>
> > Subject: Re: [AMBER] Fwd: query with amber
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID: <fa880702-f2ee-7b61-5e18-ffb2af741e5b.cgl.ucsf.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > I have no MPI experience, but can you run other MPI jobs on that machine
> > or those machines? Does
> >
> > $ locate libmpi_f90.so.0
> >
> > show the presence of the file? Does /usr/lib64/openmpi/lib have that
> > file or anything else indicating a successful install in it?
> >
> > Also on the PATH, should it be $AMBERHOME/bin ?
> >
> > Bill
> >
> >
> > On 9/13/16 11:00 PM, Pooja Kesari wrote:
> >> Dear All,
> >> I have a query regarding amber installation
> >> My amber folder is located in
> >> /usr/bin/amber11/
> >>
> >> in my tcshrc file i have defined the path
> >>
> >> setenv AMBERHOME "/usr/local/amber11"
> >> set PATH=($path $AMBERHOME)
> >> setenv LD_LIBRARY_PATH "/usr/lib64/openmpi/lib"
> >> set path = ($path $LD_LIBRARY_PATH)
> >>
> >> 1. now if i run a job it says
> >> *mpirun -np 60 sander.MPI -O -i prod.in <http://prod.in> -o
> >> prod_complex-solv.out -p complex-solv.prmtop -c protein_solv-equil.rst
> -r
> >> protein_solv-prod.rst -x prod.mdcrd -ref protein_solv-equil.rst *
> >> ------------------------------------------------------------
> --------------
> >> mpirun was unable to launch the specified application as it could not
> find
> >> an executable:
> >> Executable: sander.MPI
> >> while attempting to start process rank 0.
> >>
> >> 2. If i defined the path of sander mpi it says
> >> *mpirun -np 60 /usr/local/amber11/bin/sander.MPI -O -i prod.in
> >> <http://prod.in> -o prod_complex-solv.out -p complex-solv.prmtop -c
> >> protein_solv-equil.rst -r protein_solv-prod.rst -x prod.mdcrd -ref
> >> protein_solv-equil.rst *
> >> /usr/local/amber11/bin/sander.MPI: error while loading shared
> libraries:
> >> libmpi_f90.so.0: cannot open shared object file: No such file or
> directory
> >> /usr/local/amber11/bin/sander.MPI: error while loading shared
> libraries:
> >> libmpi_f90.so.0: cannot open shared object file: No such file or
> directory
> >> /usr/local/amber11/bin/sander.MPI: error while loading shared
> libraries:
> >> libmpi_f90.so.0: cannot open shared object file: No such file or
> directory
> >> /usr/local/amber11/bin/sander.MPI: error while loading shared
> libraries:
> >> libmpi_f90.so.0: cannot open shared object file: No such file or
> directory
> >> /usr/local/amber11/bin/sander.MPI: error while loading shared
> libraries:
> >> libmpi_f90.so.0: cannot open shared object file: No such file or
> directory
> >>
> >> Please help
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Wed, 14 Sep 2016 12:42:40 +0530
> > From: Pooja Kesari <pkesari88.gmail.com>
> > Subject: Re: [AMBER] Fwd: query with amber
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <CAH1aNEC_ymy+CA2xbbhSJMMJMhFmn+P5xMGmLymYeAtuP2GoHA.mail.
> gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Dear Bill
> > [user3.mcuserver ~]$ locate libmpi_f90.so.0
> >
> > /usr/lib64/compat-openmpi/lib/libmpi_f90.so.0
> > /usr/lib64/compat-openmpi/lib/libmpi_f90.so.0.0.1
> > /usr/lib64/compat-openmpi-psm/lib/libmpi_f90.so.0
> > /usr/lib64/compat-openmpi-psm/lib/libmpi_f90.so.0.0.1
> > /usr/local/amber11/AmberTools/src/openmpi-1.4.5/build/ompi/
> mpi/f90/.libs/libmpi_f90.so.0
> > /usr/local/amber11/AmberTools/src/openmpi-1.4.5/build/ompi/
> mpi/f90/.libs/libmpi_f90.so.0.1.0
> > /usr/local/amber11/AmberTools/src/openmpi-1.4.5/build/ompi/
> mpi/f90/.libs/libmpi_f90.so.0.1.0T
> > /usr/local/lib/libmpi_f90.so.0
> > /usr/local/lib/libmpi_f90.so.0.1.0
> >
> >
> >
> > However my library is also found in
> > /usr/lib64/openmpi/lib
> >
> > but even if i change this path to
> > setenv LD_LIBRARY_PATH /usr/lib64/compat-openmpi/lib/
> > set path = ($path $LD_LIBRARY_PATH)
> >
> > it is showing same error
> >
> > On Wed, Sep 14, 2016 at 12:09 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> I have no MPI experience, but can you run other MPI jobs on that machine
> >> or those machines? Does
> >>
> >> $ locate libmpi_f90.so.0
> >>
> >> show the presence of the file? Does /usr/lib64/openmpi/lib have that
> >> file or anything else indicating a successful install in it?
> >>
> >> Also on the PATH, should it be $AMBERHOME/bin ?
> >>
> >> Bill
> >>
> >>
> >> On 9/13/16 11:00 PM, Pooja Kesari wrote:
> >> > Dear All,
> >> > I have a query regarding amber installation
> >> > My amber folder is located in
> >> > /usr/bin/amber11/
> >> >
> >> > in my tcshrc file i have defined the path
> >> >
> >> > setenv AMBERHOME "/usr/local/amber11"
> >> > set PATH=($path $AMBERHOME)
> >> > setenv LD_LIBRARY_PATH "/usr/lib64/openmpi/lib"
> >> > set path = ($path $LD_LIBRARY_PATH)
> >> >
> >> > 1. now if i run a job it says
> >> > *mpirun -np 60 sander.MPI -O -i prod.in <http://prod.in> -o
> >> > prod_complex-solv.out -p complex-solv.prmtop -c
> protein_solv-equil.rst -r
> >> > protein_solv-prod.rst -x prod.mdcrd -ref protein_solv-equil.rst *
> >> > ------------------------------------------------------------
> >> --------------
> >> > mpirun was unable to launch the specified application as it could not
> >> find
> >> > an executable:
> >> > Executable: sander.MPI
> >> > while attempting to start process rank 0.
> >> >
> >> > 2. If i defined the path of sander mpi it says
> >> > *mpirun -np 60 /usr/local/amber11/bin/sander.MPI -O -i prod.in
> >> > <http://prod.in> -o prod_complex-solv.out -p complex-solv.prmtop -c
> >> > protein_solv-equil.rst -r protein_solv-prod.rst -x prod.mdcrd -ref
> >> > protein_solv-equil.rst *
> >> > /usr/local/amber11/bin/sander.MPI: error while loading shared
> libraries:
> >> > libmpi_f90.so.0: cannot open shared object file: No such file or
> >> directory
> >> > /usr/local/amber11/bin/sander.MPI: error while loading shared
> libraries:
> >> > libmpi_f90.so.0: cannot open shared object file: No such file or
> >> directory
> >> > /usr/local/amber11/bin/sander.MPI: error while loading shared
> libraries:
> >> > libmpi_f90.so.0: cannot open shared object file: No such file or
> >> directory
> >> > /usr/local/amber11/bin/sander.MPI: error while loading shared
> libraries:
> >> > libmpi_f90.so.0: cannot open shared object file: No such file or
> >> directory
> >> > /usr/local/amber11/bin/sander.MPI: error while loading shared
> libraries:
> >> > libmpi_f90.so.0: cannot open shared object file: No such file or
> >> directory
> >> >
> >> > Please help
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > 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
> >>
> >
> >
> >
> > --
> > Thanks & Regards,
> > Pooja Kesari
> > Research Scholar
> > Department Of Biotechnology
> > Indian Institute of Technology Roorkee
> > INDIA
> >
> >
> > ------------------------------
> >
> > Message: 7
> > Date: Wed, 14 Sep 2016 01:27:07 -0700
> > From: Bill Ross <ross.cgl.ucsf.edu>
> > Subject: Re: [AMBER] Fwd: query with amber
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID: <755e6322-f429-d937-595c-89ef0ea9e0c4.cgl.ucsf.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > Are you running on multiple machines that may not have the libs in the
> > same place? I'd expect the error msgs to say so, so I doubt it. I am out
> > of ideas. The one thing you could blindly try is using $AMBERHOME/bin in
> > your path, but I doubt that would solve it.
> >
> > Bill
> >
> >
> > On 9/14/16 12:12 AM, Pooja Kesari wrote:
> >> Dear Bill
> >> [user3.mcuserver ~]$ locate libmpi_f90.so.0
> >>
> >> /usr/lib64/compat-openmpi/lib/libmpi_f90.so.0
> >> /usr/lib64/compat-openmpi/lib/libmpi_f90.so.0.0.1
> >> /usr/lib64/compat-openmpi-psm/lib/libmpi_f90.so.0
> >> /usr/lib64/compat-openmpi-psm/lib/libmpi_f90.so.0.0.1
> >> /usr/local/amber11/AmberTools/src/openmpi-1.4.5/build/ompi/
> mpi/f90/.libs/libmpi_f90.so.0
> >> /usr/local/amber11/AmberTools/src/openmpi-1.4.5/build/ompi/
> mpi/f90/.libs/libmpi_f90.so.0.1.0
> >> /usr/local/amber11/AmberTools/src/openmpi-1.4.5/build/ompi/
> mpi/f90/.libs/libmpi_f90.so.0.1.0T
> >> /usr/local/lib/libmpi_f90.so.0
> >> /usr/local/lib/libmpi_f90.so.0.1.0
> >>
> >>
> >>
> >> However my library is also found in
> >> /usr/lib64/openmpi/lib
> >>
> >> but even if i change this path to
> >> setenv LD_LIBRARY_PATH /usr/lib64/compat-openmpi/lib/
> >> set path = ($path $LD_LIBRARY_PATH)
> >>
> >> it is showing same error
> >>
> >> On Wed, Sep 14, 2016 at 12:09 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >>
> >>> I have no MPI experience, but can you run other MPI jobs on that
> machine
> >>> or those machines? Does
> >>>
> >>> $ locate libmpi_f90.so.0
> >>>
> >>> show the presence of the file? Does /usr/lib64/openmpi/lib have that
> >>> file or anything else indicating a successful install in it?
> >>>
> >>> Also on the PATH, should it be $AMBERHOME/bin ?
> >>>
> >>> Bill
> >>>
> >>>
> >>> On 9/13/16 11:00 PM, Pooja Kesari wrote:
> >>>> Dear All,
> >>>> I have a query regarding amber installation
> >>>> My amber folder is located in
> >>>> /usr/bin/amber11/
> >>>>
> >>>> in my tcshrc file i have defined the path
> >>>>
> >>>> setenv AMBERHOME "/usr/local/amber11"
> >>>> set PATH=($path $AMBERHOME)
> >>>> setenv LD_LIBRARY_PATH "/usr/lib64/openmpi/lib"
> >>>> set path = ($path $LD_LIBRARY_PATH)
> >>>>
> >>>> 1. now if i run a job it says
> >>>> *mpirun -np 60 sander.MPI -O -i prod.in <http://prod.in> -o
> >>>> prod_complex-solv.out -p complex-solv.prmtop -c
> protein_solv-equil.rst -r
> >>>> protein_solv-prod.rst -x prod.mdcrd -ref protein_solv-equil.rst *
> >>>> ------------------------------------------------------------
> >>> --------------
> >>>> mpirun was unable to launch the specified application as it could not
> >>> find
> >>>> an executable:
> >>>> Executable: sander.MPI
> >>>> while attempting to start process rank 0.
> >>>>
> >>>> 2. If i defined the path of sander mpi it says
> >>>> *mpirun -np 60 /usr/local/amber11/bin/sander.MPI -O -i prod.in
> >>>> <http://prod.in> -o prod_complex-solv.out -p complex-solv.prmtop -c
> >>>> protein_solv-equil.rst -r protein_solv-prod.rst -x prod.mdcrd -ref
> >>>> protein_solv-equil.rst *
> >>>> /usr/local/amber11/bin/sander.MPI: error while loading shared
> libraries:
> >>>> libmpi_f90.so.0: cannot open shared object file: No such file or
> >>> directory
> >>>> /usr/local/amber11/bin/sander.MPI: error while loading shared
> libraries:
> >>>> libmpi_f90.so.0: cannot open shared object file: No such file or
> >>> directory
> >>>> /usr/local/amber11/bin/sander.MPI: error while loading shared
> libraries:
> >>>> libmpi_f90.so.0: cannot open shared object file: No such file or
> >>> directory
> >>>> /usr/local/amber11/bin/sander.MPI: error while loading shared
> libraries:
> >>>> libmpi_f90.so.0: cannot open shared object file: No such file or
> >>> directory
> >>>> /usr/local/amber11/bin/sander.MPI: error while loading shared
> libraries:
> >>>> libmpi_f90.so.0: cannot open shared object file: No such file or
> >>> directory
> >>>> Please help
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> 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: 8
> > Date: Wed, 14 Sep 2016 06:02:12 -0400
> > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > Subject: Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy
> > calculations
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <CAGk3s-REtiJf68Wa_kYHk4B_6qekn6JXzr-Lm49t=hrPPJFDDQ.
> mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > I'm not sure what you're asking, but the standard deviation is a measure
> of
> > the distribution of values you obtain, not the uncertainty in the
> average.
> > Any ensemble will have a variety of data points, but the average may
> still
> > be well known. If you want to know how reliable your average or mean is,
> > you'll need to do analysis on the error in the mean, which it seem you
> > haven't yet done. Then you can tell how precise your free energy
> > predictions are.
> >
> > On Sep 14, 2016 1:30 AM, "hari krishna" <haricoolguy111.gmail.com>
> wrote:
> >
> >> Hi all,
> >>
> >> We have carried microsecond simulations for a protein (800 aa) - RNA
> (17
> >> bp) systems. Various modified RNA molecules have been used to find the
> >> binding specificity/affinity with the same protein. The free energy of
> >> binding was calculated using MM-PBSA method. The entropic contribution
> was
> >> calculated using NMODE method. The free energy values (dG) are in the
> >> range of -250 kcal/mol. However, among the various systems used, the
> >> difference in the free energy values(ddG) are in the range of 10 to 30
> >> kcal/mol. These numbers are more or less to similar to the standard
> >> deviation of the free energy obtained MM-PBSA calculations. Are these
> >> error values obtained from the calculations quantitatively correct? Is
> it
> >> safe to report such free energy changes in publications. If not, is
> there
> >> any other better way to calculate the absolute free energy other than
> >> approximation methods using AMBER package?
> >>
> >> Harikrishna
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > ------------------------------
> >
> > Message: 9
> > Date: Wed, 14 Sep 2016 12:06:57 +0200
> > From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
> > Subject: [AMBER] How to "not" strip an ion (say Mg) in MMPBSA
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <CAPKknGoX6Em4mDJpP-6yyPPmc6Di80DJ6fJsBgEuhYFUe4wv
> 3w.mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi,
> >
> > I am trzying to calculate binding energy between two proteins using
> MMPBSA
> > method. I found that all ions were automatically deleted by ptraj.
> However,
> > I want to keep Mg2+ intact in my system. How can I do this.
> >
> > Thanks,
> > Hirdesh
> >
> >
> > ------------------------------
> >
> > Message: 10
> > Date: Wed, 14 Sep 2016 11:06:44 +0000
> > From: Anna Cebrian Prats <Anna.Cebrian.uab.cat>
> > Subject: [AMBER] Force field ff14SB
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> >
> > <AM5PR0701MB294786F383BC2B98AF728C638AF10.AM5PR0701MB2947.
> eurprd07.prod.outlook.com>
> >
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hi amber users,
> >
> >
> > I have a question about the ff14SB force field.
> >
> >
> > I want to know, if the 1-4 non-bonded interactions scale value (1.2)
> > instead of 2.0 used in the ff94 (old version) is also included in
> > the ff14SB? if not, which electrostatic scaling factor automatically
> > use this force field?
> >
> >
> > Thank you
> >
> >
> > Anna
> >
> >
> > ------------------------------
> >
> > Message: 11
> > Date: Wed, 14 Sep 2016 14:36:42 +0100
> > From: David A Case <david.case.rutgers.edu>
> > Subject: Re: [AMBER] Fullerene RESP charges derivation
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID: <20160914133642.GA31091.scarletmail.rutgers.edu>
> > Content-Type: text/plain; charset=us-ascii
> >
> > On Tue, Sep 13, 2016, Fabio Bologna wrote:
> >>
> >> I've computed the ESP charges for an endohedral metallofullerene (
> >> GdC82) using Gaussian09 and the following input line:
> >>
> >> Info: the number of the path atoms exceeds MAXPATHATOMNUM(xxx) for atom
> >> [0], extend the size and reallocate the memory automatically.
> >>
> >> The message then continued to reappear no-stop, with the xxx number
> >> always growing and the atom number always 0. Does anyone know the reason
> >> for this behavior? Could it be that the structure of the carbon cage
> >> confuses the program because it doesn't have "a start and an end"?
> >
> > This sounds likely. But be sure to visualize the pdb file you are
> sending
> > to Amber, to make sure that it looks OK.
> >
> > ....dac
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 12
> > Date: Wed, 14 Sep 2016 14:40:52 +0100
> > From: David A Case <david.case.rutgers.edu>
> > Subject: Re: [AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have
> > a type. Failed to generate parameters Parameter file was not
> saved.
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID: <20160914134052.GB31091.scarletmail.rutgers.edu>
> > Content-Type: text/plain; charset=us-ascii
> >
> > On Wed, Sep 14, 2016, shahab shariati wrote:
> >
> >> FATAL: Atom .R<CLEU 124>.A<H04 25> does not have a type.
> >
> > To expand on Bill's email, this means that you have an atom named
> > "H04" in the
> > pdb file, which is not in the CLEU library unit. You need to fix the
> > residue and atom naming in the pdb file.
> >
> > [Developers: can someone update this error message to make things
> clearer?
> > Same thing for the "Creating new atom..." message. Ideally, there would
> be a
> > counter, so that the extended help message is only printed once.]
> >
> > ...dac
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 13
> > Date: Wed, 14 Sep 2016 14:49:43 +0100
> > From: David A Case <david.case.rutgers.edu>
> > Subject: Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy
> > calculations
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID: <20160914134943.GC31091.scarletmail.rutgers.edu>
> > Content-Type: text/plain; charset=us-ascii
> >
> > On Wed, Sep 14, 2016, hari krishna wrote:
> >>
> >> We have carried microsecond simulations for a protein (800 aa) - RNA
> (17
> >> bp) systems. Various modified RNA molecules have been used to find the
> >> binding specificity/affinity with the same protein. The free energy of
> >> binding was calculated using MM-PBSA method. The entropic contribution
> was
> >> calculated using NMODE method. The free energy values (dG) are in the
> >> range of -250 kcal/mol.
> >
> > It's not clear from your email what you mean by "dG": is this the
> estimated
> > value for the protein-RNA association energy? If so, something is
> seriously
> > amiss. If you are making errors of hundreds of kcal/mol in the aboslute
> > binding affinities, it's hard to be sure that these errors will all
> cancel
> > in the ddG calculations.
> >
> > I understand that many people in our field assume that there will be
> > this sort
> > of error cancelation, so that ddG values might be useful even where the
> > underlying dG values are not. But I have never been at all happy with
> this
> > idea: there is a fair likelihood that some really important feature
> (specific
> > metal ion effects?) is missing from the model.
> >
> > .....dac
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 14
> > Date: Wed, 14 Sep 2016 14:54:41 +0100
> > From: David A Case <david.case.rutgers.edu>
> > Subject: Re: [AMBER] Fwd: query with amber
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID: <20160914135441.GD31091.scarletmail.rutgers.edu>
> > Content-Type: text/plain; charset=us-ascii
> >
> > On Wed, Sep 14, 2016, Pooja Kesari wrote:
> >>
> >> setenv AMBERHOME "/usr/local/amber11"
> >> set PATH=($path $AMBERHOME)
> >
> > Should be $AMBERHOME/bin, not $AMBERHOME.
> >
> >> setenv LD_LIBRARY_PATH "/usr/lib64/openmpi/lib"
> >> set path = ($path $LD_LIBRARY_PATH)
> >
> > It looks like you built openmpi from $AMBERHOME/AmberTools/src. In this
> > case, you need to include $AMBERHOME/lib in the LD_LIBRARY_PATH.
> >
> > Even better: upgrade to AmberTools16 (it's free). Installation is much
> > simpler now than it was ten years ago, and many bugs have been fixed.
> >
> > ....dac
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 15
> > Date: Wed, 14 Sep 2016 14:18:52 +0000
> > From: Fabio Bologna <fabio.bologna2.studio.unibo.it>
> > Subject: [AMBER] R: Fullerene RESP charges derivation
> > To: "david.case.rutgers.edu" <david.case.rutgers.edu>, AMBER Mailing
> > List <amber.ambermd.org>
> > Message-ID:
> >
> > <AM4PR0101MB168199B66EDE39D1E39174CF91F10.AM4PR0101MB1681.
> eurprd01.prod.exchangelabs.com>
> >
> > Content-Type: text/plain; charset="windows-1256"
> >
> > I've taken a look at the pdb and the structure is sound.... Now I'm
> > trying to compute the charges for the anionic fullerene cage to see
> > if the problem is related to the metal ion inside
> >
> > Inviata dal mio Windows Phone
> > ________________________________
> > Da: David A Case<mailto:david.case.rutgers.edu>
> > Inviato: ?14/?09/?2016 15:39
> > A: AMBER Mailing List<mailto:amber.ambermd.org>
> > Oggetto: Re: [AMBER] Fullerene RESP charges derivation
> >
> > On Tue, Sep 13, 2016, Fabio Bologna wrote:
> >>
> >> I've computed the ESP charges for an endohedral metallofullerene (
> >> GdC82) using Gaussian09 and the following input line:
> >>
> >> Info: the number of the path atoms exceeds MAXPATHATOMNUM(xxx) for atom
> >> [0], extend the size and reallocate the memory automatically.
> >>
> >> The message then continued to reappear no-stop, with the xxx number
> >> always growing and the atom number always 0. Does anyone know the reason
> >> for this behavior? Could it be that the structure of the carbon cage
> >> confuses the program because it doesn't have "a start and an end"?
> >
> > This sounds likely. But be sure to visualize the pdb file you are
> sending
> > to Amber, to make sure that it looks OK.
> >
> > ....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > ------------------------------
> >
> > Message: 16
> > Date: Wed, 14 Sep 2016 22:31:29 +0800
> > From: Dd H <ddhecnu.gmail.com>
> > Subject: [AMBER] Parameters for GppNHp ligand.
> > To: AMBER <amber.ambermd.org>
> > Message-ID:
> > <CACGt4etgQzYAofhpZVc72U85Mf8RThdSCcQ+fYv-m+W8b1CS8A.mail.
> gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi,
> > I want to do a MD simulation of a protein-ligand complex. The ligand is a
> > GppNHp, an analogue to GTP. My question is how to get the parameter set
> for
> > this molecule?
> > Thank you in advance!
> >
> > Dading Huang
> >
> >
> > ------------------------------
> >
> > Message: 17
> > Date: Wed, 14 Sep 2016 16:57:36 +0200
> > From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
> > Subject: Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy
> > calculations
> > To: <amber.ambermd.org>
> > Message-ID: <726dbb42-e947-b65d-e9c3-f017617cdef7.mpi-muenster.mpg.de>
> > Content-Type: text/plain; charset="windows-1252"; format=flowed
> >
> > In some threads a while ago, we had numerous discussions about doing
> > MMPBSA on protein-nucleic acids interactions ...I agree with Dave that
> > values of -250 kcal/mol (assuming the dG represents the binding
> > affinity) are very far away from the correct values to be reliable for
> > estimating ddGs ! Possibly, some of the problems lie in the protocol you
> > are using. In particular, the default values for a lots of parameters in
> > MMPBSA in Amber 15 or older are not suitable for protein-nucleic acids
> > interactions (I did not run yet MMPBSA with Amber 16) ....
> >
> > In this paper (http://www.ncbi.nlm.nih.gov/pubmed/25126959), we present
> > similar calculations for a protein-DNA complex with absolute values
> > (Table 3) that for some of the protocols we tried are much closer to the
> > experimental values. The values are very sensitive to a lots of
> > different input parameters.
> >
> > Best wishes
> > Vlad
> >
> > On 09/14/2016 03:49 PM, David A Case wrote:
> >> On Wed, Sep 14, 2016, hari krishna wrote:
> >>> We have carried microsecond simulations for a protein (800 aa) - RNA
> (17
> >>> bp) systems. Various modified RNA molecules have been used to find the
> >>> binding specificity/affinity with the same protein. The free energy of
> >>> binding was calculated using MM-PBSA method. The entropic contribution
> was
> >>> calculated using NMODE method. The free energy values (dG) are in the
> >>> range of -250 kcal/mol.
> >> It's not clear from your email what you mean by "dG": is this the
> estimated
> >> value for the protein-RNA association energy? If so, something is
> seriously
> >> amiss. If you are making errors of hundreds of kcal/mol in the aboslute
> >> binding affinities, it's hard to be sure that these errors will all
> cancel
> >> in the ddG calculations.
> >>
> >> I understand that many people in our field assume that there will
> >> be this sort
> >> of error cancelation, so that ddG values might be useful even where the
> >> underlying dG values are not. But I have never been at all happy with
> this
> >> idea: there is a fair likelihood that some really important feature
> >> (specific
> >> metal ion effects?) is missing from the model.
> >>
> >> .....dac
> >>
> >>
> >> _______________________________________________
> >> 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: 18
> > Date: Wed, 14 Sep 2016 12:13:52 -0300
> > From: Bruno Falcone <brunofalcone.qo.fcen.uba.ar>
> > Subject: Re: [AMBER] How to "not" strip an ion (say Mg) in MMPBSA
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID: <361315b9-67ca-04d4-3cc4-ab77670fee08.qo.fcen.uba.ar>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > Hi Hirdesh,
> >
> > as far as I know, MMPBSA doesn't automatically strip anything, you have
> > to explicitly tell it to do so.
> > Can you share with us the input you're using so that we can track the
> > error? Perhaps you're stripping the Mg2+ ions with ante-MMPBSA?
> >
> > Cheers,
> > Bruno
> >
> > On 14/09/16 07:06, Hirdesh Kumar wrote:
> >> Hi,
> >>
> >> I am trzying to calculate binding energy between two proteins using
> MMPBSA
> >> method. I found that all ions were automatically deleted by ptraj.
> However,
> >> I want to keep Mg2+ intact in my system. How can I do this.
> >>
> >> Thanks,
> >> Hirdesh
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 19
> > Date: Wed, 14 Sep 2016 11:58:20 -0400
> > From: Jason Swails <jason.swails.gmail.com>
> > Subject: Re: [AMBER] How to "not" strip an ion (say Mg) in MMPBSA
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <CAEk9e3oZ=j1G3nNfW3dfaNi-RiocC8_XY3wXSpQ2Ujfp7VyyJw.
> mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > On Wed, Sep 14, 2016 at 6:06 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> I am trzying to calculate binding energy between two proteins using
> MMPBSA
> >> method. I found that all ions were automatically deleted by ptraj.
> However,
> >> I want to keep Mg2+ intact in my system. How can I do this.
> >>
> >
> > ?Two options:
> >
> > 1. Set the strip_mask variable to explicitly omit the ion you want to
> keep
> > 2. Pre-process the trajectory with cpptraj first to prevent MMPBSA.py
> from
> > stripping any solvent
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> >
> >
> > ------------------------------
> >
> > Message: 20
> > Date: Wed, 14 Sep 2016 12:00:34 -0400
> > From: Jason Swails <jason.swails.gmail.com>
> > Subject: Re: [AMBER] Force field ff14SB
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <CAEk9e3qwCJWy47p5NbO4JOUBFu7Fce-eAdCZvEZMgzMfqxDpvw.mail.
> gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > On Wed, Sep 14, 2016 at 7:06 AM, Anna Cebrian Prats <
> Anna.Cebrian.uab.cat>
> > wrote:
> >
> >> Hi amber users,
> >>
> >>
> >> I have a question about the ff14SB force field.
> >>
> >>
> >> I want to know, if the 1-4 non-bonded interactions scale value (1.2)
> >> instead of 2.0 used in the ff94 (old version) is also included in the
> >> ff14SB? if not, which electrostatic scaling factor automatically use
> this
> >> force field?
> >>
> >
> > ?ff14SB uses the same scaling factor as ff94 -- 1.2. The value 2.0 was
> > used *before* ff94 I believe (ff94 is the root ancestor of the line of
> FFs
> > ff96, ff99, ff99SB, ff12SB, and ff14SB), and all of those force fields
> have
> > the same charges and electrostatic scaling factors.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> >
> >
> > ------------------------------
> >
> > Message: 21
> > Date: Wed, 14 Sep 2016 12:05:33 -0400
> > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > Subject: Re: [AMBER] Force field ff14SB
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <CAGk3s-RtFYDt=nsbknqh3Hw4CAJS54WptZjhQSQ4WzYdXqe2nw.mail.
> gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > To add to Jason's correct reply, when you say "non-bonded interactions"
> > make sure to distinguish between 1-4 scaling factors for electrostatic
> and
> > for vdw interactions.
> >
> > On Sep 14, 2016 12:00 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
> >
> >> On Wed, Sep 14, 2016 at 7:06 AM, Anna Cebrian Prats <
> Anna.Cebrian.uab.cat>
> >> wrote:
> >>
> >> > Hi amber users,
> >> >
> >> >
> >> > I have a question about the ff14SB force field.
> >> >
> >> >
> >> > I want to know, if the 1-4 non-bonded interactions scale value (1.2)
> >> > instead of 2.0 used in the ff94 (old version) is also included in the
> >> > ff14SB? if not, which electrostatic scaling factor automatically use
> this
> >> > force field?
> >> >
> >>
> >> ?ff14SB uses the same scaling factor as ff94 -- 1.2. The value 2.0 was
> >> used *before* ff94 I believe (ff94 is the root ancestor of the line of
> FFs
> >> ff96, ff99, ff99SB, ff12SB, and ff14SB), and all of those force fields
> have
> >> the same charges and electrostatic scaling factors.
> >>
> >> HTH,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > ------------------------------
> >
> > Message: 22
> > Date: Wed, 14 Sep 2016 16:11:16 +0000
> > From: Anna Cebrian Prats <Anna.Cebrian.uab.cat>
> > Subject: Re: [AMBER] Force field ff14SB
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> >
> > <AM5PR0701MB294772A094713A3D89CACC968AF10.AM5PR0701MB2947.
> eurprd07.prod.outlook.com>
> >
> > Content-Type: text/plain; charset="us-ascii"
> >
> > okey thank you!! [?]
> >
> > ________________________________
> > De: Carlos Simmerling <carlos.simmerling.gmail.com>
> > Enviat el: dimecres, 14 de setembre de 2016 18:05:33
> > Per a: AMBER Mailing List
> > Tema: Re: [AMBER] Force field ff14SB
> >
> > To add to Jason's correct reply, when you say "non-bonded interactions"
> > make sure to distinguish between 1-4 scaling factors for electrostatic
> and
> > for vdw interactions.
> >
> > On Sep 14, 2016 12:00 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
> >
> >> On Wed, Sep 14, 2016 at 7:06 AM, Anna Cebrian Prats <
> Anna.Cebrian.uab.cat>
> >> wrote:
> >>
> >> > Hi amber users,
> >> >
> >> >
> >> > I have a question about the ff14SB force field.
> >> >
> >> >
> >> > I want to know, if the 1-4 non-bonded interactions scale value (1.2)
> >> > instead of 2.0 used in the ff94 (old version) is also included in the
> >> > ff14SB? if not, which electrostatic scaling factor automatically use
> this
> >> > force field?
> >> >
> >>
> >> ?ff14SB uses the same scaling factor as ff94 -- 1.2. The value 2.0 was
> >> used *before* ff94 I believe (ff94 is the root ancestor of the line of
> FFs
> >> ff96, ff99, ff99SB, ff12SB, and ff14SB), and all of those force fields
> have
> >> the same charges and electrostatic scaling factors.
> >>
> >> HTH,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> _______________________________________________
> >> 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: 23
> > Date: Wed, 14 Sep 2016 23:24:13 +0530
> > From: hari krishna <haricoolguy111.gmail.com>
> > Subject: Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy
> > calculations
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <CADa8WMoWA11QBqBCJP1hXQptmR-k+DRbw_8GT=52no2jx=huWQ.mail.
> gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Dear Professor,
> >
> > Thank you very much for the reply. To be clear, my question, whether the
> > MMPBSA method is reliable in calculating the binding energy for such a
> > large system.
> >
> >
> > Harikrishna
> >
> >
> >
> >
> > I'm not sure what you're asking, but the standard deviation is a measure
> of
> > the distribution of values you obtain, not the uncertainty in the
> average.
> > Any ensemble will have a variety of data points, but the average may
> still
> > be well known. If you want to know how reliable your average or mean is,
> > you'll need to do analysis on the error in the mean, which it seem you
> > haven't yet done. Then you can tell how precise your free energy
> > predictions are.
> >
> > On Sep 14, 2016 1:30 AM, "hari krishna" <haricoolguy111.gmail.com>
> wrote:
> >
> > *> Hi all, *
> > *> *
> > *> We have carried microsecond simulations for a protein (800 aa) - RNA
> > (17 *
> > *> bp) systems. Various modified RNA molecules have been used to find
> the *
> > *> binding specificity/affinity with the same protein. The free energy
> of *
> > *> binding was calculated using MM-PBSA method. The entropic contribution
> > was *
> > *> calculated using NMODE method. The free energy values (dG) are in the
> *
> > *> range of -250 kcal/mol. However, among the various systems used, the *
> > *> difference in the free energy values(ddG) are in the range of 10 to
> 30 *
> > *> kcal/mol. These numbers are more or less to similar to the standard *
> > *> deviation of the free energy obtained MM-PBSA calculations. Are these
> *
> > *> error values obtained from the calculations quantitatively correct? Is
> > it *
> > *> safe to report such free energy changes in publications. If not, is
> > there *
> > *> any other better way to calculate the absolute free energy other than
> *
> > *> approximation methods using AMBER package? *
> > *> *
> > *> Harikrishna *
> > *> _______________________________________________ *
> > *> AMBER mailing list *
> > *> AMBER.ambermd.org <http://AMBER.ambermd.org> *
> > *> http://lists.ambermd.org/mailman/listinfo/amber
> > <http://lists.ambermd.org/mailman/listinfo/amber> *
> > *> *
> >
> > On Wed, Sep 14, 2016 at 11:00 AM, hari krishna <haricoolguy111.gmail.com
> >
> > wrote:
> >
> >> Hi all,
> >>
> >> We have carried microsecond simulations for a protein (800 aa) - RNA
> (17
> >> bp) systems. Various modified RNA molecules have been used to find the
> >> binding specificity/affinity with the same protein. The free energy of
> >> binding was calculated using MM-PBSA method. The entropic contribution
> was
> >> calculated using NMODE method. The free energy values (dG) are in the
> >> range of -250 kcal/mol. However, among the various systems used, the
> >> difference in the free energy values(ddG) are in the range of 10 to 30
> >> kcal/mol. These numbers are more or less to similar to the standard
> >> deviation of the free energy obtained MM-PBSA calculations. Are these
> >> error values obtained from the calculations quantitatively correct? Is
> it
> >> safe to report such free energy changes in publications. If not, is
> there
> >> any other better way to calculate the absolute free energy other than
> >> approximation methods using AMBER package?
> >>
> >> Harikrishna
> >>
> >
> >
> > ------------------------------
> >
> > Message: 24
> > Date: Wed, 14 Sep 2016 20:27:16 +0200 (MEST)
> > From: Jiri Sponer <sponer.ncbr.muni.cz>
> > Subject: Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy
> > calculations
> > To: AMBER Mailing List <amber.ambermd.org>
> > Cc: haricoolguy111.gmail.com
> > Message-ID: <Pine.NEB.4.64.1609142020070.6567.ncbr.ncbr.muni.cz>
> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
> >
> > Dear hari krishna:
> >
> > you can find recent analysis of approximations
> > in continuum solvent binding studies in this review
> > paper:
> >
> > The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
> > By: Genheden, Samuel; Ryde, Ulf
> > EXPERT OPINION ON DRUG DISCOVERY Volume: 10 Issue: 5 Pages: 449-461
> > Published: MAY 2015
> >
> > Protein/RNA complexes can be even more difficult even for
> > basic simulations.
> >
> > Can We Execute Stable Microsecond-Scale Atomistic Simulations of
> > Protein-RNA Complexes?
> > By: Krepl, M.; Havrila, M.; Stadlbauer, P.; et al.
> > JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 11 Issue: 3
> > Pages: 1220-1243 Published: MAR 2015
> >
> > all the best Jiri
> >
> > -------------------------------------------------------
> > Jiri Sponer
> > Institute of Biophysics
> > Academy of Sciences of the Czech Republic
> > Kralovopolska 135
> > CZ-61265 Brno
> > Czech Republic
> > e-mail: sponer.ncbr.muni.cz
> > fax: 420 5412 12179
> > phone: 420 5415 17133
> > http://www.ibp.cz/
> > http://www.ibp.cz/en/departments/structure-and-
> dynamics-of-nucleic-acids/
> > -----------------------------------------------------------
> >
> >
> >
> >
> >
> > On Wed, 14 Sep 2016, hari krishna wrote:
> >
> >> Date: Wed, 14 Sep 2016 23:24:13 +0530
> >> From: hari krishna <haricoolguy111.gmail.com>
> >> Reply-To: AMBER Mailing List <amber.ambermd.org>
> >> To: AMBER Mailing List <amber.ambermd.org>
> >> Subject: Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy
> calculations
> >>
> >> Dear Professor,
> >>
> >> Thank you very much for the reply. To be clear, my question, whether the
> >> MMPBSA method is reliable in calculating the binding energy for such a
> >> large system.
> >>
> >>
> >> Harikrishna
> >>
> >>
> >>
> >>
> >> I'm not sure what you're asking, but the standard deviation is a
> measure of
> >> the distribution of values you obtain, not the uncertainty in the
> average.
> >> Any ensemble will have a variety of data points, but the average may
> still
> >> be well known. If you want to know how reliable your average or mean is,
> >> you'll need to do analysis on the error in the mean, which it seem you
> >> haven't yet done. Then you can tell how precise your free energy
> >> predictions are.
> >>
> >> On Sep 14, 2016 1:30 AM, "hari krishna" <haricoolguy111.gmail.com>
> wrote:
> >>
> >> *> Hi all, *
> >> *> *
> >> *> We have carried microsecond simulations for a protein (800 aa) - RNA
> >> (17 *
> >> *> bp) systems. Various modified RNA molecules have been used to find
> the *
> >> *> binding specificity/affinity with the same protein. The free energy
> of *
> >> *> binding was calculated using MM-PBSA method. The entropic
> contribution
> >> was *
> >> *> calculated using NMODE method. The free energy values (dG) are in
> the *
> >> *> range of -250 kcal/mol. However, among the various systems used, the
> *
> >> *> difference in the free energy values(ddG) are in the range of 10 to
> 30 *
> >> *> kcal/mol. These numbers are more or less to similar to the standard *
> >> *> deviation of the free energy obtained MM-PBSA calculations. Are
> these *
> >> *> error values obtained from the calculations quantitatively correct?
> Is
> >> it *
> >> *> safe to report such free energy changes in publications. If not, is
> >> there *
> >> *> any other better way to calculate the absolute free energy other
> than *
> >> *> approximation methods using AMBER package? *
> >> *> *
> >> *> Harikrishna *
> >> *> _______________________________________________ *
> >> *> AMBER mailing list *
> >> *> AMBER.ambermd.org <http://AMBER.ambermd.org> *
> >> *> http://lists.ambermd.org/mailman/listinfo/amber
> >> <http://lists.ambermd.org/mailman/listinfo/amber> *
> >> *> *
> >>
> >> On Wed, Sep 14, 2016 at 11:00 AM, hari krishna <
> haricoolguy111.gmail.com>
> >> wrote:
> >>
> >>> Hi all,
> >>>
> >>> We have carried microsecond simulations for a protein (800 aa) - RNA
> (17
> >>> bp) systems. Various modified RNA molecules have been used to find the
> >>> binding specificity/affinity with the same protein. The free energy of
> >>> binding was calculated using MM-PBSA method. The entropic contribution
> was
> >>> calculated using NMODE method. The free energy values (dG) are in the
> >>> range of -250 kcal/mol. However, among the various systems used, the
> >>> difference in the free energy values(ddG) are in the range of 10 to 30
> >>> kcal/mol. These numbers are more or less to similar to the standard
> >>> deviation of the free energy obtained MM-PBSA calculations. Are these
> >>> error values obtained from the calculations quantitatively correct? Is
> it
> >>> safe to report such free energy changes in publications. If not, is
> there
> >>> any other better way to calculate the absolute free energy other than
> >>> approximation methods using AMBER package?
> >>>
> >>> Harikrishna
>
>
>
>
> F.-Y. Dupradeau
> ---
> http://q4md-forcefieldtools.org/FyD/
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 20 2016 - 02:30:03 PDT
