Quoting Lachele Foley <lf.list.gmail.com>:
> Just for completeness: GLYCAM06 is much better than GLYCAM04...
please read: http://q4md-forcefieldtools.org/REDDB/projects/F-85/
http://www.ncbi.nlm.nih.gov/pubmed/21792425?dopt=Abstract
regards, F.
> 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/
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 20 2016 - 06:00:02 PDT
