Hi Daniel,
Thanks very much. I'll let you know when I try it.
Ahmed
On Thu, Mar 13, 2014 at 1:00 PM, <amber-request.ambermd.org> wrote:
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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: reg: the charges for methylated cytosine atoms (David A Case)
> 2. Re: 3DRISM and orientationally averaged 3D pair distribution
> functions (T Luchko (Lists))
> 3. Re: reg: the charges for methylated cytosine atoms (Sidney Elmer)
> 4. problem with -make-mdins mode in entropy MMPBSA.py.MPI
> calculations (Marek Maly)
> 5. Re: problem with -make-mdins mode in entropy MMPBSA.py.MPI
> calculations (Jason Swails)
> 6. Re: problem with -make-mdins mode in entropy MMPBSA.py.MPI
> calculations (Marek Maly)
> 7. AmberTools update 24 for CPPTRAJ (Daniel Roe)
> 8. Re: MMPBSA TrajError (Daniel Roe)
> 9. Re: non-bonded parameters for ferric iron and ferrous iron
> (Pengfei Li)
> 10. Re: Help for system configuration (Ross Walker)
> 11. Re: problem with -make-mdins mode in entropy MMPBSA.py.MPI
> calculations (Jason Swails)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 12 Mar 2014 15:33:59 -0400
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] reg: the charges for methylated cytosine atoms
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20140312193359.GD90000.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Wed, Mar 12, 2014, Sidney Elmer wrote:
>
> > This information was very helpful. I would like to build double
> > stranded DNA with methylated cytosines directly in NAB using bdna().
> > I looked through the NAB code and quickly got lost. I'm happy to do
> > this myself, but I would appreciate some guidance as to how to do
> > this. Could someone please outline the steps necessary to accomplish
> > this? Thank you!
>
> First, use NAB to build a standard BNDA helix [use fd_helix(), not bdna()].
> See tutorial B1 for a detailed walk-through on how to do this.
> An easier alternative for most cases is to visit w3dna.rutgers.edu.
>
> Second, edit the PDB file to change the DC residue names to whatever your
> library is calling methylated cytosine; let LEaP build the structure from
> the un-methylated structure.
>
> ...good luck...dac
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 12 Mar 2014 13:07:12 -0700
> From: "T Luchko (Lists)" <tluchko.lists.gmail.com>
> Subject: Re: [AMBER] 3DRISM and orientationally averaged 3D pair
> distribution functions
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <E9EF825C-9CA8-45A4-92BA-3D12D1F9CE17.gmail.com>
> Content-Type: text/plain; charset=windows-1252
>
> It is possible to do this but I haven?t personally written anything for
> full spherical orientational averaging. I do have code for cylindrical
> averaging. Contact me directly if you would like a copy.
>
> Tyler
>
> On Mar 12, 2014, at 11:34 AM, Brian Radak <radak004.umn.edu> wrote:
>
> > Is it possible to get orientationally averaged pair distribution
> functions
> > from rism3d.snglpnt? By this I mean:
> >
> > g(r) = (1/(4pi)) int dW g(*r*)
> >
> > where W is the solid angle and g(*r*) is the 3d pair distribution
> function
> > from --guv on the command line (I think that normalization is correct).
> > This is essentially a series of surface integrals, but I'd rather not
> write
> > code to do them if I don't have to.
> >
> > Ultimately what I want is the effective cutoff where the density of some
> > species is equal to the bulk.
> >
> > Thanks,
> > Brian
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Center for
> Integrative
> > Proteomics Room 308
> > Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 12 Mar 2014 17:01:58 -0700
> From: Sidney Elmer <paulymer.gmail.com>
> Subject: Re: [AMBER] reg: the charges for methylated cytosine atoms
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAM_WORqF_ActS946Dm=
> K+469igo21XxQtM+SrcVmxqLey-m3Yg.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Thank you for the suggestion, David.
>
> There were two gotchas that other's might hit, just like I did:
>
> 1. don't forget to delete the H5 atom in your pdb file
> 2. in order to make the parameters compatible with the amber99SBildn
> force field, I had to change the atom type for the C5' atom to CT
>
>
>
>
> On Wed, Mar 12, 2014 at 12:33 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
>
> > On Wed, Mar 12, 2014, Sidney Elmer wrote:
> >
> > > This information was very helpful. I would like to build double
> > > stranded DNA with methylated cytosines directly in NAB using bdna().
> > > I looked through the NAB code and quickly got lost. I'm happy to do
> > > this myself, but I would appreciate some guidance as to how to do
> > > this. Could someone please outline the steps necessary to accomplish
> > > this? Thank you!
> >
> > First, use NAB to build a standard BNDA helix [use fd_helix(), not
> bdna()].
> > See tutorial B1 for a detailed walk-through on how to do this.
> > An easier alternative for most cases is to visit w3dna.rutgers.edu.
> >
> > Second, edit the PDB file to change the DC residue names to whatever your
> > library is calling methylated cytosine; let LEaP build the structure from
> > the un-methylated structure.
> >
> > ...good luck...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 13 Mar 2014 01:40:12 +0100
> From: "Marek Maly" <marek.maly.ujep.cz>
> Subject: [AMBER] problem with -make-mdins mode in entropy
> MMPBSA.py.MPI calculations
> To: amber.ambermd.org
> Message-ID: <op.xcmxhafplc8gdf.pocitadlon.ujep.cz>
> Content-Type: text/plain; charset=iso-8859-2; format=flowed; delsp=yes
>
> Dear all,
>
> I had recently some problems with receptor entropy
> calculations (minimization phase) using MMPBSA.py.MPI
> so I wanted to check/edit relevant parameters so I
> used -make-mdins in the command hoping to obtain
> input files:
>
> _MMPBSA_sander_nm_min.mdin
> _MMPBSA_nmode.in
>
> But MMPBSA.py.MPI as well as MMPBSA.py program
> just wrote these two lines and exited.
>
> ----------------------------------------------------
> Loading and checking parameter files for compatibility...
> Created mdin files. Quitting.
> ---------------------------------------------------
>
> No mdin files was created in spite the information written by
> the program.
>
> Interestingly, this problem appears just in case of entropy calculation.
> If I switch to PB,GB or APBS calculation, the -make-mdins flag works
> perfectly and relevant mdin files (_MMPBSA_gb.mdin,_MMPBSA_pb.mdin ...)
> are successfully
> created.
>
> I am using patched actual version of Ambertools13 and Amber12 and I tested
> this issue on two
> different machines and also on two different molecular systems.
>
> Thank you in advance for any useful comments.
>
> Best wishes,
>
> Marek
>
> PS: Here is for the completeness my in file:
>
> &general
> receptor_mask=:11-80
> ligand_mask=:1-10
> startframe=1
> keep_files=2, debug_printlevel=2,
> /
> &nmode
> nmode_igb=0, nmode_istrng=0.0, nminterval=167,
> maxcyc=100000, drms=0.1,
> /
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
> Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery:
> http://www.opera.com/mail/
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 12 Mar 2014 21:24:35 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] problem with -make-mdins mode in entropy
> MMPBSA.py.MPI calculations
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3qqpvoEFnsftouuVFyBA1=
> Qh6EXmZr_ed6P3_GfTjRDmQ.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Wed, Mar 12, 2014 at 8:40 PM, Marek Maly <marek.maly.ujep.cz> wrote:
>
> > Dear all,
> >
> > I had recently some problems with receptor entropy
> > calculations (minimization phase) using MMPBSA.py.MPI
> > so I wanted to check/edit relevant parameters so I
> > used -make-mdins in the command hoping to obtain
> > input files:
> >
> > _MMPBSA_sander_nm_min.mdin
> > _MMPBSA_nmode.in
> >
> > But MMPBSA.py.MPI as well as MMPBSA.py program
> > just wrote these two lines and exited.
> >
> > ----------------------------------------------------
> > Loading and checking parameter files for compatibility...
> > Created mdin files. Quitting.
> > ---------------------------------------------------
> >
> > No mdin files was created in spite the information written by
> > the program.
> >
> > Interestingly, this problem appears just in case of entropy calculation.
> > If I switch to PB,GB or APBS calculation, the -make-mdins flag works
> > perfectly and relevant mdin files (_MMPBSA_gb.mdin,_MMPBSA_pb.mdin ...)
> > are successfully
> > created.
> >
> > I am using patched actual version of Ambertools13 and Amber12 and I
> tested
> > this issue on two
> > different machines and also on two different molecular systems.
> >
>
> MMPBSA.py does not use input files for normal mode entropy calculations.
> All available options are exposed in the &nmode section of the input file.
> The input files you referred to above were written for minimizing
> snapshots in sander and running normal mode calculations with the nmode
> program.
>
> Normal mode calculations are now run with a nab program that is invoked
> through command-line flags.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 13 Mar 2014 14:58:05 +0100
> From: "Marek Maly" <marek.maly.ujep.cz>
> Subject: Re: [AMBER] problem with -make-mdins mode in entropy
> MMPBSA.py.MPI calculations
> To: "AMBER Mailing List" <amber.ambermd.org>
> Message-ID: <op.xcnye3ldlc8gdf.pocitadlon.ujep.cz>
> Content-Type: text/plain; charset=iso-8859-2; format=flowed; delsp=yes
>
> Thanks Jason,
>
> so at this moment if one would like to change some advanced/additional
> settings in case of entropy calculation using MMPBSA.py he may
> do it perhaps just via those command-line flags (they are perhaps
> described in NAB documentation ? ) which are used for the command based
> invoking of the NAB program,
> from MMPBSA.py script am I right ?
>
>
> The second possibility if one would like to "play" more with all entropy
> associated
> parameters he may use directly NAB (not NAB called from MMPBSA.py) to
> calculate entropy
> of his system. Am I right ?
>
> Best wishes,
>
> Marek
>
>
>
>
> Dne Thu, 13 Mar 2014 02:24:35 +0100 Jason Swails <jason.swails.gmail.com>
> napsal/-a:
>
> > On Wed, Mar 12, 2014 at 8:40 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> >
> >> Dear all,
> >>
> >> I had recently some problems with receptor entropy
> >> calculations (minimization phase) using MMPBSA.py.MPI
> >> so I wanted to check/edit relevant parameters so I
> >> used -make-mdins in the command hoping to obtain
> >> input files:
> >>
> >> _MMPBSA_sander_nm_min.mdin
> >> _MMPBSA_nmode.in
> >>
> >> But MMPBSA.py.MPI as well as MMPBSA.py program
> >> just wrote these two lines and exited.
> >>
> >> ----------------------------------------------------
> >> Loading and checking parameter files for compatibility...
> >> Created mdin files. Quitting.
> >> ---------------------------------------------------
> >>
> >> No mdin files was created in spite the information written by
> >> the program.
> >>
> >> Interestingly, this problem appears just in case of entropy calculation.
> >> If I switch to PB,GB or APBS calculation, the -make-mdins flag works
> >> perfectly and relevant mdin files (_MMPBSA_gb.mdin,_MMPBSA_pb.mdin ...)
> >> are successfully
> >> created.
> >>
> >> I am using patched actual version of Ambertools13 and Amber12 and I
> >> tested
> >> this issue on two
> >> different machines and also on two different molecular systems.
> >>
> >
> > MMPBSA.py does not use input files for normal mode entropy calculations.
> > All available options are exposed in the &nmode section of the input
> > file.
> > The input files you referred to above were written for minimizing
> > snapshots in sander and running normal mode calculations with the nmode
> > program.
> >
> > Normal mode calculations are now run with a nab program that is invoked
> > through command-line flags.
> >
> > HTH,
> > Jason
> >
>
>
> --
> Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery:
> http://www.opera.com/mail/
>
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 13 Mar 2014 08:35:58 -0600
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: [AMBER] AmberTools update 24 for CPPTRAJ
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAAC0qOaoWVdBkRUuEc+zbHJiOoSryp+T-kGUUmgXNXhQzbD7Yg.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi All,
>
> I would like to announce update 24 for AmberTools 13, which contains minor
> bug fixes for CPPTRAJ:
>
> 1) In 'nastruct', fix small error in calculation of number of hydrogen
> bonds between base pairs; only affects first frame when the given residue
> range is not continuous.
>
> 2) Fix a bug that was causing number of frames to be not properly detected
> in Gzipped Amber trajectory files larger than 4 GB.
>
> This update is currently available. To apply, simply re-run configure from
> $AMBERHOME and re-compile.
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
>
> ------------------------------
>
> Message: 8
> Date: Thu, 13 Mar 2014 08:37:30 -0600
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] MMPBSA TrajError
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOb8uVbx3PmaxsCQpSzttZyJhs20kpXoMEsn9uwen=
> wt4Q.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
>
> This bug should be fixed by AmberTools 13 update 24, now available. If you
> get a chance to try out the patch please let me know if it fixes the
> problem you were having. Thanks again for the report.
>
> -Dan
>
>
> On Tue, Mar 11, 2014 at 10:41 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi,
> >
> > I can confirm that there appears to be a bug in version 13 that is not
> > present in 12 that prevents cpptraj from determining the correct number
> of
> > frames in a compressed trajectory. I am still testing to be sure, but
> this
> > may only be an issue with large compressed trajectories. While this does
> > not affect reading frames in cpptraj (i.e. actions in cpptraj itself will
> > work fine), it does cause problems for MMPBSA since version 13 cpptraj
> > isn't reporting the number of frames for these compressed trajectories. I
> > am currently working on a fix. Thanks for the report.
> >
> > -Dan
> >
> >
> > On Tue, Mar 11, 2014 at 10:07 PM, Daniel Roe <daniel.r.roe.gmail.com
> >wrote:
> >
> >> Hi,
> >>
> >> Do the compressed trajectories actually contain 500 frames? That is to
> >> say, if you unzip one of the trajectories and load it into cpptraj (or
> even
> >> ptraj) does it still say 500 frames?
> >>
> >> Thanks,
> >>
> >> -Dan
> >>
> >>
> >> On Tue, Mar 11, 2014 at 2:14 PM, Ahmed Ayoub <atayoub.ualberta.ca>
> wrote:
> >>
> >>> Hi Daniel,
> >>>
> >>> Here is the input and output of the old cpptraj version. It is worth
> >>> mentioning that the trajectories were generated using Amber 12.18 GPU
> >>> cuda
> >>> version.
> >>>
> >>> *input:*
> >>>
> >>>
> >>>
> >>>
> >>> *trajin ../Mprod6.mdcrd.gz 1 100000 4trajin ../Mprod7.mdcrd.gz 1 100000
> >>> 4trajin ../Mprod8.mdcrd.gz 1 100000 4trajin ../Mprod9.mdcrd.gz 1 100000
> >>> 4trajout prod6-9.nc <http://prod6-9.nc> netcdf*
> >>>
> >>> *output (old version):*
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> *CPPTRAJ: Trajectory Analysis. V12.4 ___ ___ ___ ___ | \/ |
> \/
> >>> |
> >>> \/ | _|_/\_|_/\_|_/\_|_INPUT: Reading Input from file traj.in
> >>> <http://traj.in> [trajin ../Mprod6.mdcrd.gz 1 100000 4]
> >>> [Mprod6.mdcrd.gz] contains 500 frames. Warning: Mprod6.mdcrd.gz stop
> >>> 100000 >= #Frames (500), setting to max. [trajin ../Mprod7.mdcrd.gz 1
> >>> 100000 4] [Mprod7.mdcrd.gz] contains 500 frames. Warning:
> >>> Mprod7.mdcrd.gz stop 100000 >= #Frames (500), setting to max. [trajin
> >>> ../Mprod8.mdcrd.gz 1 100000 4] [Mprod8.mdcrd.gz] contains 500
> >>> frames. Warning: Mprod8.mdcrd.gz stop 100000 >= #Frames (500),
> setting
> >>> to max. [trajin ../Mprod9.mdcrd.gz 1 100000 4]
> [Mprod9.mdcrd.gz]
> >>> contains 500 frames. Warning: Mprod9.mdcrd.gz stop 100000 >= #Frames
> >>> (500), setting to max. [trajout prod6-9.nc <http://prod6-9.nc>
> >>> netcdf]INPUT TRAJECTORIES: [Mprod6.mdcrd.gz] is an AMBER trajectory,
> >>> Parm
> >>> 0 (with box info) (reading 125 of 500) [Mprod7.mdcrd.gz] is an AMBER
> >>> trajectory, Parm 0 (with box info) (reading 125 of 500)
> >>> [Mprod8.mdcrd.gz]
> >>> is an AMBER trajectory, Parm 0 (with box info) (reading 125 of 500)
> >>> [Mprod9.mdcrd.gz] is an AMBER trajectory, Parm 0 (with box info)
> (reading
> >>> 125 of 500) Coordinate processing will occur on 500 frames.PARAMETER
> >>> FILES: 0: ../com-wat.top, 379197 atoms, 119489 res, ortho. box, 117759
> >>> mol,
> >>> 117250 solvent mol, 500 framesREFERENCE COORDS: No reference
> >>> coordinates.
> >>> No frames defined.OUTPUT TRAJECTORIES: [prod6-9.nc <http://prod6-9.nc
> >]
> >>> is
> >>> a NetCDF AMBER trajectory, Parm 0: Writing 500 framesACTIONS:
> >>> Initializing
> >>> 0 actions:BEGIN TRAJECTORY
> >>> PROCESSING:.....................................................PARM
> >>> [com-wat.top]: Setting up 0 actions.----- [Mprod6.mdcrd.gz] (1-497, 4)
> >>> -----*
> >>> * 0% ....etc*
> >>>
> >>>
> >>> *Output (New version):*
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> *CPPTRAJ: Trajectory Analysis. V13.22 ___ ___ ___ ___ | \/ |
> >>> \/ |
> >>> \/ | _|_/\_|_/\_|_/\_|_ AmberParm Title: [default_name]
> >>> Radius Set: H(N)-modified Bondi radii (mbondi2)INPUT: Reading Input
> from
> >>> file traj_new.in <http://traj_new.in> [trajin ../Mprod6.mdcrd.gz 1
> >>> 100000
> >>> 4]Warning: Mprod6.mdcrd.gz: Number of frames in compressed traj could
> not
> >>> be determined. Frames will be read until EOF.
> >>> [Mprod6.mdcrd.gz] contains an unknown number of frames. [trajin
> >>> ../Mprod7.mdcrd.gz 1 100000 4]Warning: Mprod7.mdcrd.gz: Number of
> frames
> >>> in
> >>> compressed traj could not be determined. Frames will be read
> >>> until
> >>> EOF. [Mprod7.mdcrd.gz] contains an unknown number of frames.
> >>> [trajin ../Mprod8.mdcrd.gz 1 100000 4]Warning: Mprod8.mdcrd.gz: Number
> of
> >>> frames in compressed traj could not be determined. Frames will
> be
> >>> read until EOF. [Mprod8.mdcrd.gz] contains an unknown number of
> >>> frames. [trajin ../Mprod9.mdcrd.gz 1 100000 4]Warning:
> Mprod9.mdcrd.gz:
> >>> Number of frames in compressed traj could not be determined.
> >>> Frames
> >>> will be read until EOF. [Mprod9.mdcrd.gz] contains an unknown
> >>> number
> >>> of frames. [trajout prod6-9_new.nc <http://prod6-9_new.nc>
> >>> netcdf]PARAMETER FILES: 0: com-wat.top, 379197 atoms, 119489 res, box:
> >>> Orthogonal, 117759 mol, 117250 solvent, 100000 framesINPUT
> TRAJECTORIES:
> >>> 0:
> >>> [Mprod6.mdcrd.gz] is an AMBER trajectory, Parm com-wat.top (Orthogonal
> >>> box)
> >>> (reading 25000) 1: [Mprod7.mdcrd.gz] is an AMBER trajectory, Parm
> >>> com-wat.top (Orthogonal box) (reading 25000) 2: [Mprod8.mdcrd.gz] is an
> >>> AMBER trajectory, Parm com-wat.top (Orthogonal box) (reading 25000) 3:
> >>> [Mprod9.mdcrd.gz] is an AMBER trajectory, Parm com-wat.top (Orthogonal
> >>> box)
> >>> (reading 25000) Coordinate processing will occur on 100000
> >>> frames.REFERENCE COORDS: No frames defined.OUTPUT TRAJECTORIES:
> >>> [prod6-9_new.nc <http://prod6-9_new.nc>] is a NetCDF AMBER trajectory,
> >>> Parm
> >>> com-wat.top: Writing 100000 frames (1-Last, 1)BEGIN TRAJECTORY
> >>> PROCESSING:----- [Mprod6.mdcrd.gz] (1-99997, 4) -----*
> >>> * 0% .....etc*
> >>>
> >>>
> >>>
> >>> Message: 1
> >>> Date: Fri, 7 Mar 2014 13:02:04 -0700
> >>> From: Daniel Roe <daniel.r.roe.gmail.com>
> >>> Subject: Re: [AMBER] MMPBSA TrajError
> >>> To: AMBER Mailing List <amber.ambermd.org>
> >>> Message-ID:
> >>> <CAAC0qOa-Ooo5LDeiN3kMSgO2K+_
> >>> Hv7CALXYU_t=fvcBA_WwLCA.mail.gmail.com>
> >>> Content-Type: text/plain; charset=ISO-8859-1
> >>>
> >>> Hi,
> >>>
> >>> On Fri, Mar 7, 2014 at 12:32 PM, Ahmed Ayoub <atayoub.ualberta.ca>
> >>> wrote:
> >>>
> >>> > and the MMPBSA.py I'm using is a relatively new one. I made sure of
> >>> that
> >>> by
> >>> > running cpptraj from the new AmberTools build and it was unable to
> read
> >>> the
> >>> > number of frames.
> >>> >
> >>>
> >>> This is odd, there should be no version incompatibilities with
> trajectory
> >>> formats for any version of cpptraj since the trajectory formats have
> not
> >>> changed. Can you give me the exact cpptraj input and output for the old
> >>> and
> >>> new versions?
> >>>
> >>> -Dan
> >>>
> >>>
> >>> > The workaround was to save the coordinates once more using the new
> >>> build
> >>> > cpptraj so that it can be understood by the new MMPBSA.py.
> >>> >
> >>> > Thanks for your help.
> >>> >
> >>> > Ahmed Ayoub
> >>> > _______________________________________________
> >>> > AMBER mailing list
> >>> > AMBER.ambermd.org
> >>> > http://lists.ambermd.org/mailman/listinfo/amber
> >>> >
> >>>
> >>>
> >>>
> >>> --
> >>> -------------------------
> >>> Daniel R. Roe, PhD
> >>> Department of Medicinal Chemistry
> >>> University of Utah
> >>> 30 South 2000 East, Room 201
> >>> Salt Lake City, UT 84112-5820
> >>> http://home.chpc.utah.edu/~cheatham/
> >>> (801) 587-9652
> >>> (801) 585-6208 (Fax)
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 201
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
>
> ------------------------------
>
> Message: 9
> Date: Thu, 13 Mar 2014 11:31:44 -0400
> From: Pengfei Li <ambermailpengfei.gmail.com>
> Subject: Re: [AMBER] non-bonded parameters for ferric iron and ferrous
> iron
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CACMvKPY1V3DbsYgXXayhqENXryK9_+OTyiW2Xq3SYu8gD83+jQ.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Jean-Paul,
>
> I have started the project for parameterization of trivalent metal ions in
> TIP3P water model. When I get the results, I will send you an email.
>
> All the best,
> Pengfei
>
>
>
> 2014-03-10 4:03 GMT-04:00 JPB <jpb.q4md-forcefieldtools.org>:
>
> > Hi Kennie and Pengfei,
> >
> > My favorite water model is tip3p.
> > It would be nice if you could start with this one.
> > Thanks for your consideration.
> >
> > Cheers.
> > JPB.
> >
> >
> > Ken Merz <kmerz1.gmail.com> a ?crit :
> >
> > > Hi,
> > >
> > > The 12-6-4 will be in the next AMBER release, so you can access
> > > this technology once the new version is out. In the meantime we dug
> > > up the coordination numbers, ion-oxygen distances and hydration free
> > > energies for a range of M(III) species. If you have a water model
> > > that is your favorite we can focus on this model first using both
> > > the 12-6 model and the 12-6-4 for Fe(III). Once we have this in hand
> > > we can jump to the other water models to generate the full story.
> > >
> > > Hope this helps,
> > >
> > > Kennie
> > >
> > >
> > > On Mar 7, 2014, at 11:07 AM, JPB <jpb.q4md-forcefieldtools.org> wrote:
> > >
> > >> Hi Pengfei,
> > >>
> > >> I was not talking about building a topology with Fe2+,
> > >> I don't really need help on this one.
> > >>
> > >> My point is to build upon an existing model
> > >> of a bioinorganic complex containing Fe3+
> > >> and improve it by using state of the art description
> > >> of the LJ potential.
> > >> Hence, I am planning to use the LJ potential you introduced in your
> > >> 2014 JCTC.
> > >> The problem is I do not have access to the version of
> > >> the pmemd(?) program in which you implemented this new potential.
> > >> So, to put it brief, it would be great, if we could collaborate on
> this
> > one
> > >> and you could give me the opportunity to access a version of pmemd
> > >> working with the modified non-bonded potential.
> > >> I also understood that you are currently developing the parameters
> > >> for Fe3+ which are the ones I am interested in.
> > >>
> > >> Cheers.
> > >> JPB.
> > >>
> > >>
> > >>
> > >> Pengfei Li <ambermailpengfei.gmail.com> a ?crit :
> > >>
> > >>> Hi Jean-Paul,
> > >>>
> > >>> 2014-03-06 9:47 GMT-05:00 Jean-Paul Becker <
> > jpb.q4md-forcefieldtools.org>:
> > >>>
> > >>>> Hi Pengfei,
> > >>>>
> > >>>> It will certainly not surprise you that one of my major concern is
> > time.
> > >>>> It seems that between the parametrization and the availability of
> > >>>> the potential in Amber14, it can be within more than a couple of
> > >>>> months from now.
> > >>>> My dynamics are currently running with the 'old' parameters and I
> > >>>> would have liked
> > >>>> to have the opportunity to assess your development right away.
> > >>>
> > >>> I will be glad if you can send the parameters to me as soon as you
> > >>> get them.
> > >>>>
> > >>>
> > >>> No problem. Since the parameters may be different for different water
> > >>> models.
> > >>> Can you tell me which kind of water model are you using in the
> > simulation?
> > >>> I can design that set of parameters with priority. I will send you
> the
> > >>> parameters when
> > >>> we get them.
> > >>>
> > >>>
> > >>>> By the way, with your agreement, they can be a great addition to the
> > RED
> > >>>> DB.
> > >>>>
> > >>>
> > >>> Yeah, go ahead. It has been published, feel free to add this into the
> > RED
> > >>> DB.
> > >>>
> > >>> Cheers.
> > >>>> JPB.
> > >>>>
> > >>>
> > >>> All the best,
> > >>> Pengfei
> > >>>
> > >>>
> > >>>>
> > >>>>
> > >>>>
> > >>>> Pengfei Li <ambermailpengfei.gmail.com> a ?crit :
> > >>>>
> > >>>>> Hi Jean-Peul,
> > >>>>>
> > >>>>> The 12-6-4 model has been added to Amber 14 as a new feature which
> > will
> > >>>> be
> > >>>>> released in the coming April. For the Fe3+ ion, the 12-6-4
> > >>>> parameterization
> > >>>>> work is undergoing in our group. Since there are also other
> projects
> > >>>>> undergoing, it may take some time for us to get it (and if you are
> > >>>>> interested in, we can send you the parameter after we get it). Hope
> > this
> > >>>>> helps, if you have more questions or concerns, please tell me.
> > >>>>>
> > >>>>> All the best,
> > >>>>> Pengfei
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>> 2014-03-05 16:11 GMT-05:00 Jean-Paul Becker <
> > >>>> jpb.q4md-forcefieldtools.org>:
> > >>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>> ----- Message transf?r? de jean-paul.becker.u-picardie.fr -----
> > >>>>>> Date : Wed, 05 Mar 2014 20:32:24 +0100
> > >>>>>> De : Jean-Paul Becker <jean-paul.becker.u-picardie.fr>
> > >>>>>> Objet : Re: [AMBER] non-bonded parameters for ferric iron and
> > ferrous
> > >>>>>> iron
> > >>>>>> ? : AMBER Mailing List <amber.ambermd.org>, Ken Merz <
> > >>>>>> kmerz1.gmail.com>
> > >>>>>> Cc : Pengfei Li <ldsoar1990.gmail.com>
> > >>>>>>
> > >>>>>> Hi Kennie,
> > >>>>>>
> > >>>>>> Thanks for the answer.
> > >>>>>> Regarding the topology of the bonded model we took advantage of
> our
> > >>>>>> RED server and especialy its new version written in Python.
> > >>>>>> However, I would be very curions and interested to use your LJ
> > params
> > >>>>>> for trivalent cations (ferric iron) on our model and ?valuate how
> > they
> > >>>>>> perform.
> > >>>>>> Right now, I am not sure which way to proceed, I don't know how
> much
> > >>>>>> it implies
> > >>>>>> to use 12-6-4 model within Amber.
> > >>>>>> Cheers.
> > >>>>>> JPB
> > >>>>>>
> > >>>>>> Ken Merz <kmerz1.gmail.com> a ?crit :
> > >>>>>>
> > >>>>>>> Hi,
> > >>>>>>> We created LJ params for the ferrous iron, but not ferric
> > >>>>>>> (http://pubs.acs.org/doi/abs/10.1021/ct400146w and
> > >>>>>>>
> > >>>>>>
> > >>>>
> >
> http://pubs.acs.org/doi/abs/10.1021/ct400751u?prevSearch=pengfei%2Bli&searchHistoryKey=
> > >>>> ).
> > >>>>>> We might be willing to create these for you if you are
> dissatisfied
> > with
> > >>>>>> what is out there. We can create a 12-6 or a 12-6-4 model
> depending
> > on
> > >>>> how
> > >>>>>> you want to proceed. To create a bonded model for the coordination
> > >>>>>> environment you can use MCPB. Good luck,
> > >>>>>>> Kennie
> > >>>>>>>
> > >>>>>>> On Mar 4, 2014, at 12:08 PM, Jean-Paul Becker
> > >>>>>>> <jpb.q4md-forcefieldtools.org> wrote:
> > >>>>>>>
> > >>>>>>>> Dear Amber users,
> > >>>>>>>>
> > >>>>>>>> I searched the bibbliography for non-bonded parameters for
> > >>>>>>>> a five-coordinate ferric iron.
> > >>>>>>>>
> > >>>>>>>> There are the well known values coming from D.A. Giammona's PhD
> > >>>>>>>> thesis (1.2 and 0.05)
> > >>>>>>>> that were once in the Amber contrib but removed recently.
> > >>>>>>>> These values are said to be appropriate for a six-coordinate
> iron
> > >>>>>> though.
> > >>>>>>>>
> > >>>>>>>> In the supporting information of Shahrokh et al. (J. Comput.
> Chem.
> > >>>>>>>> 33:119-133,2012)
> > >>>>>>>> one can find three sets of non-bonded parameters either for
> > ferrous
> > >>>>>> iron or
> > >>>>>>>> ferric iron in different environment:
> > >>>>>>>> 1.8 0.01
> > >>>>>>>> 1.3 0.002
> > >>>>>>>> 1.3 0.01
> > >>>>>>>> but reading the paper, the method used to derive these
> parameters
> > >>>> does
> > >>>>>>>> not appear clearly.
> > >>>>>>>>
> > >>>>>>>> In Shahrokh et al., a reference leads to Moore et al.
> > >>>>>>>> (Biochemistry 49:9011-9019,1010) where one can read:
> > >>>>>>>> "The van der Waals parameters for the heme iron atom were
> manually
> > >>>>>>>> assigne Rii
> > >>>>>>>> and epsii values of 1.3 and 0.01, respectively."...
> > >>>>>>>>
> > >>>>>>>> I am wondering where to look for published and trustworthy
> > non-bonded
> > >>>>>>>> parameteres suitable
> > >>>>>>>> to ferric iron in a five-coordinate environment.
> > >>>>>>>> My question is also more general and applies to ferrous and
> ferric
> > >>>>>>>> iron in five-coodinate
> > >>>>>>>> and six-coordinates environmants as well.
> > >>>>>>>> Any suggestion would be deeply appreciated.
> > >>>>>>>>
> > >>>>>>>> Cheers.
> > >>>>>>>> JPB.
> > >>>>>>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>> _______________________________________________
> > >>>> 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
> > >
> > > Kenneth M. Merz, Jr.
> > > Director, Institute for Cyber Enabled Research (iCER)
> > > Editor-in-Chief, Journal of Chemical Information and Modeling
> > > Joseph Zichis Chair in Chemistry
> > > Department of Chemistry
> > > Department of Biochemistry and Molecular Biology
> > > Michigan State University
> > > 578 S. Shaw Lane
> > > East Lansing, MI 48824-1322
> > >
> > > Phone: 517-355-9715 (Chemistry)
> > > 517-884-2540 (iCER)
> > > 517-353-7248 (Fax)
> > > Cell: 814-360-0376
> > >
> > > e-mail: kmerz1.gmail.com
> > > http://www.merzgroup.org/
> > > https://icer.msu.edu
> > > iCER Help: https://contact.icer.msu.edu/contact
> > >
> > > However, one should bear in mind that a macromolecular refinement
> > > against high resolution data is never finished, only abandoned.
> > >
> > > George Sheldrick (2008), Acta Crystallogr. D64 112-122.
> > >
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> Pengfei Li
> Ph.D. Candidate
> Merz Research Group
> Department of Chemistry
> Michigan State University
>
>
> ------------------------------
>
> Message: 10
> Date: Thu, 13 Mar 2014 08:50:09 -0700
> From: Ross Walker <ross.rosswalker.co.uk>
> Subject: Re: [AMBER] Help for system configuration
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <CF4721B5.3C809%ross.rosswalker.co.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> Yes if your motherboard supports it.
>
>
>
> On 3/12/14, 6:50 AM, "Gustavo Seabra" <gustavo.seabra.gmail.com> wrote:
>
> >Hi Ross,
> >
> >Will P2P support work out-of-the-box on current GPU cards (such as GTX
> >780)?
> >
> >Gustavo Seabra
> >
> >
> >
> >On Mar 11, 2014, at 8:57 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> >
> >> It will work with PCI-E gen 2 x16 just not as well as Gen 3 - Existing
> >> GPUs, say up to K40 will probably be ok in Gen 2 - beyond that, 780TI,
> >> Titan-Black and K... the GPUs themselves will likely be so quick that
> >>they
> >> saturate the PCI-E bus for Gen 2.
> >>
> >> Note, the nice thing with the peer to peer support is that it will run
> >> awesome on twin GPU cards - I.e. GTX690, (790 if it appears), K10 and
> >>...
> >>
> >> All the best
> >> Ross
> >>
> >>
> >>
> >> On 3/11/14, 3:31 PM, "filip fratev" <filipfratev.yahoo.com> wrote:
> >>
> >>>
> >>>
> >>> Hi Ross,
> >>> Only PCI-E gen 3 x 16 slots? What about PCI-E gen 2 x 16 slots?
> >>>
> >>> Regards,
> >>> Filip
> >>>
> >>>
> >>>
> >>>
> >>> On Wednesday, March 12, 2014 12:25 AM, Ross Walker
> >>> <ross.rosswalker.co.uk> wrote:
> >>>
> >>> Hi Kshatresh,
> >>>
> >>> What do you mean by double computational efficiency? For GPU AMBER the
> >>> performance is determined almost exclusively (with a few minor
> >>>caveats) by
> >>> the GPU. AMBER 14 will be about 30% faster than AMBER 12 across the
> >>>board
> >>> for PME calculations - substantially faster for NPT if you use the new
> >>> Monte Carlo Barostat. It will also support peer to peer across 2 x 2
> >>>GPUs
> >>> on most motherboards. That is you can run peer to peer parallel on GPUs
> >>> connected to the same IOH controller - which effectively means CPU
> >>>socket
> >>> as long as those cards are on PCI-E gen 3 x 16 slots or better. 4 way
> >>>peer
> >>> to peer will be supported at some point (the code will support it
> >>> natively) but the hardware itself does not exist yet (we are ahead of
> >>>the
> >>> hardware curve for once! :-) ).
> >>>
> >>> Let me know some more details about what you want to simulate, the sort
> >>> performance you are after and I can let you know what GPU models, what
> >>> settings etc to try. Note AMBER 14 will also support hydrogen mass
> >>> repartitioning so in principal you can run at 4fs time step. This gets
> >>>you
> >>> to around 380+ ns/day for a JAC NPT run (4fs) with two
> >>>GTX-Titan-Blacks. -
> >>> Note we are waiting on a fix from NVIDIA before the Titan Black will
> >>> actually be usable with AMBER - at present calculations diverge or
> >>>crash
> >>> within about 15 minutes or so. I am confident that a fix will be
> >>>possible
> >>> though (it was for the original Titans so stay tuned).
> >>>
> >>> All the best
> >>> Ross
> >>>
> >>>
> >>> On 3/11/14, 2:35 PM, "Kshatresh Dutta Dubey" <kshatresh.gmail.com>
> >>>wrote:
> >>>
> >>>> Thank you Dr. Ross, I will contact Mike for desired configurations.
> >>>> Although I have previous quote for Model Quantum TXR413-512R but I
> >>>>need
> >>>> almost double computational efficiency relative to that one.
> >>>> Regards
> >>>> Kshatresh
> >>>>
> >>>>
> >>>> On Tue, Mar 11, 2014 at 9:31 PM, Ross Walker <ross.rosswalker.co.uk>
> >>>> wrote:
> >>>>
> >>>>> Hi Kshatresh
> >>>>>
> >>>>> Let me put you in touch with Mike Chen at Exxact Corp (cc'd here).
> >>>>> Exxact
> >>>>> are our hardware partners for building AMBER Certified GPU machines.
> >>>>> They
> >>>>> can quote you a system that is optimized price/performance wise for
> >>>>> running AMBER. It will ship fully tested, certified and warrantied.
> >>>>> They
> >>>>> can also customize the machine to your specific requirements and
> >>>>> budget.
> >>>>>
> >>>>> Please see the following pages:
> >>>>> http://ambermd.org/gpus/recommended_hardware.htm#hardware
> >>>>>
> >>>>> and
> >>>>>
> >>>>> http://exxactcorp.com/index.php/solution/solu_list/65
> >>>>>
> >>>>> for more info.
> >>>>>
> >>>>> All the best
> >>>>> Ross
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> On 3/11/14, 9:46 AM, "Kshatresh Dutta Dubey" <kshatresh.gmail.com>
> >>>>> wrote:
> >>>>>
> >>>>>> Dear all,
> >>>>>>
> >>>>>> We have to purchase GPU machine suitable for next release of Amber
> >>>>> 14. We
> >>>>>> have to run the MD simulations for a large system (about 100K
> >>>>>>atom). I
> >>>>>> will
> >>>>>> be thankful if someone suggests me for the best configurations. Our
> >>>>> grant
> >>>>>> allows us for 20K USD.
> >>>>>> Thanks in advance
> >>>>>> Kshatresh
> >>>>>>
> >>>>>> --
> >>>>>> _______________________________________________
> >>>>>> 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
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> With best regards
> >>>>
> >>>>***********************************************************************
> >>>>**
> >>>> *
> >>>> **********************
> >>>> Dr. Kshatresh Dutta Dubey
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
> ------------------------------
>
> Message: 11
> Date: Thu, 13 Mar 2014 13:44:15 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] problem with -make-mdins mode in entropy
> MMPBSA.py.MPI calculations
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3oomy+7wDfh1khg3L20dXN4-d_hXMa2WXiD3LnCo-j=
> 4Q.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Thu, Mar 13, 2014 at 9:58 AM, Marek Maly <marek.maly.ujep.cz> wrote:
>
> > Thanks Jason,
> >
> > so at this moment if one would like to change some advanced/additional
> > settings in case of entropy calculation using MMPBSA.py he may
> > do it perhaps just via those command-line flags (they are perhaps
> > described in NAB documentation ? ) which are used for the command based
> > invoking of the NAB program,
> > from MMPBSA.py script am I right ?
> >
>
> You can try to deduce what the command-line flags are for
> mmpbsa_py_nabnmode (the program that actually gets run by MMPBSA.py to
> compute normal modes), but I don't think you'll get any added flexibility
> using the program directly compared to specifying variables in the
> MMPBSA.py input file.
>
> If you really want to customize the normal mode calculation you'll need to
> write your own nab program that performs it the way you want it performed.
> The back of the AmberTools manual describes the syntax of the NAB
> programming language (and you can use mmpbsa_entropy.nab in
> $AMBERHOME/AmberTools/src/mmpbsa_py to get started).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 792, Issue 1
> *************************************
>
>
--
Ahmed Taha Ayoub
PhD Student, Theoretical and Computational Chemistry
W4-54, Department of Chemistry
11227 Saskatchewan Drive
University of Alberta
Edmonton, Alberta T6G 2G2
Canada
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 13 2014 - 13:30:02 PDT
