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-6yyPPmc6Di80DJ6fJsBgEuhYFUe4wv3w.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
Received on Tue Sep 20 2016 - 02:00:02 PDT
