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--
Thanks & Regards,
Pooja Kesari
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------------------------------
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>
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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>
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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>
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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>
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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>
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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>
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<CAGk3s-RtFYDt=nsbknqh3Hw4CAJS54WptZjhQSQ4WzYdXqe2nw.mail.gmail.com>
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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>
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<AM5PR0701MB294772A094713A3D89CACC968AF10.AM5PR0701MB2947.eurprd07.prod.outlook.com>
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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>
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<CADa8WMoWA11QBqBCJP1hXQptmR-k+DRbw_8GT=52no2jx=huWQ.mail.gmail.com>
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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
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
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Received on Thu Sep 15 2016 - 07:30:02 PDT