Hi,
I don't have a direct answer for you. So while waiting for others to
reponse, you can have a look at AMBER tutorial about deriving several force
field parameters
http://ambermd.org/tutorials/advanced/tutorial23/
It's good to read original GAFF paper to see 'how' too:
http://onlinelibrary.wiley.com/doi/10.1002/jcc.20035/full
Note: developing FF is very extensive work.
good luck
Hai
On Tue, Mar 8, 2016 at 11:01 PM, Ruixing Wang <rwang013.e.ntu.edu.sg> wrote:
> Dear all,
>
> I'm a new who do parameterization work on GAFF, and I'm confused about how
> are the parameters determined in GAFF.
>
> 1. For example, in gaff.dat of AmberTools15 (gaff1.7, Nov 2013):
> >SOURCE3
> >Optimized geometries at MP2/6-31G* level
> >SOURCE4
> >Optimized geometries at B3LYP/6-31G* level
> How is this done? Can anyone provide some information about getting
> parameters from the QM optimized geometries?
>
> 2. For dihedrals, I searched the internet and many of the results do a PES
> scan about a dihedral. But for X -ca-ca-X , I think it's not possible to do
> a PES scan, rotating on ca-ca bond, how did gaff get this value? The source
> of this dihedral writes " intrpol.bsd.on C6H6", I don't know what it means.
>
> Hopefully someone can give some reference. Thank you very much:)
>
> Best regards,
> WANG, Ruixing
>
> end
> 2016-03-09 4:00 GMT+08:00 amber-request.ambermd.org <
> amber-request.ambermd.org>:
>
> > 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
> > 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. tests dont work for serial, parallel or cuda amber
> > instalation. (Wesley Alves)
> > 2. Re: tests dont work for serial, parallel or cuda amber
> > instalation. (Daniel Roe)
> > 3. Re: Gist calculation on clustered structures
> > (peter.schmidtke.discngine.servier.com)
> > 4. Re: cpptraj rmsd error (Orthogonal box), unknown #frames,
> > start=0 offset=1 (Saman Yousuf ali)
> > 5. Chamber tool, error using the prmtop and inpcrd files
> > (Anna Cebrian Prats)
> > 6. Re: Chamber tool, error using the prmtop and inpcrd files
> > (Jason Swails)
> > 7. pseudo trajectories for 4 centers of mass? (Hirdesh Kumar)
> > 8. Re: pseudo trajectories for 4 centers of mass? (Daniel Roe)
> > 9. How to interpret MMGBSA ligand binding free energy
> > decomposition results (Zhang Marc)
> > 10. Production phase for MMPBSA (Arati Paudyal)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 7 Mar 2016 17:20:05 -0300
> > From: Wesley Alves <wesley.diatom.gmail.com>
> > Subject: [AMBER] tests dont work for serial, parallel or cuda amber
> > instalation.
> > To: amber.ambermd.org
> > Message-ID:
> > <CAFUApsj=
> > FN3V7WO3AFgxtn5EKeZ6pUa2eAOqy3rMAW_8WH5VDw.mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi Dears,
> > I am trying to install amber14 with ambertools15, in Linux OpenSUSE
> system,
> > with AMD processor (8 cores), 32 GB of memory, NVIDIA GTX 670, and 2
> NVIDIA
> > Tesla k-20.
> >
> > I had completed the instalation of modules serial, parallel (-mpi) and
> > cuda, according the manual instructions. However, the test of all
> instaled
> > modules was failed, with the same error at make test command.
> >
> > > export DO_PARALLEL="mpirun -np 2"
> > > make test
> > (cd AmberTools/test && make test)
> > make[1]: Entering directory '/home/labime/amber14/AmberTools/test'
> > ./test_at_serial.sh
> >
> > Warning: DO_PARALLEL is set to "mpirun -np 2".
> > This environment variable is being unset for serial testing.
> >
> > ValueError: numpy.dtype has the wrong size, try recompiling
> > Makefile:6: recipe for target 'test' failed
> > make[1]: *** [test] Error 1
> > make[1]: Leaving directory '/home/labime/amber14/AmberTools/test'
> > Makefile:43: recipe for target 'test.serial' failed
> > make: *** [test.serial] Error 2
> >
> > Can you help me ???
> > Thanks for attention.
> > Wesley
> > --
> > Wesley J?nio Alves da Concei??o
> > Undergraduate Biophysics Student
> > Laboratory for Molecular Modelling and Dynamics - Carlos Chagas Filho
> > Biophysics Institute
> > Laboratory for Structural Molecular Biology - Pharmacy Faculty
> > Federal University of Rio de Janeiro
> > Rio de Janeiro - RJ
> > Brazil
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 7 Mar 2016 14:23:07 -0700
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Subject: Re: [AMBER] tests dont work for serial, parallel or cuda
> > amber instalation.
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <CAAC0qOa=
> > 1FGe60Co3E6DnmcuA7BVpciWdpKGivYjSK-R_S1NyA.mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi,
> >
> > On Mon, Mar 7, 2016 at 1:20 PM, Wesley Alves <wesley.diatom.gmail.com>
> > wrote:
> > >
> > >> export DO_PARALLEL="mpirun -np 2"
> > >> make test
> > > (cd AmberTools/test && make test)
> > > make[1]: Entering directory '/home/labime/amber14/AmberTools/test'
> > > ./test_at_serial.sh
> > >
> > > Warning: DO_PARALLEL is set to "mpirun -np 2".
> > > This environment variable is being unset for serial testing.
> >
> > Running 'make test' from $AMBERHOME will only test the last completed
> > build, which in your case is apparently the serial one. If you want to
> > run tests on all installed components (i.e. parallel, serial, cuda)
> > you should run those tests using the appropriate scripts. For example,
> > the Amber component (pmemd) tests are found in $AMBERHOME/test:
> >
> > test_amber_serial.sh: Test serial pmemd
> > test_amber_parallel.sh: Test pmemd.MPI
> > test_amber_cuda_serial.sh: Test pmemd.cuda
> >
> > etc. The AmberTools component tests are in $AMBERHOME/AmberTools/test
> > and have similarly named scripts. DO_PARALLEL only needs to be set for
> > the 'parallel' scripts.
> >
> > >
> > > ValueError: numpy.dtype has the wrong size, try recompiling
> > > Makefile:6: recipe for target 'test' failed
> > > make[1]: *** [test] Error 1
> > > make[1]: Leaving directory '/home/labime/amber14/AmberTools/test'
> > > Makefile:43: recipe for target 'test.serial' failed
> > > make: *** [test.serial] Error 2
> >
> > I think we would need some more context around this error (i.e. the
> > text leading up to the error) to debug further.
> >
> > -Dan
> >
> > >
> > > Can you help me ???
> > > Thanks for attention.
> > > Wesley
> > > --
> > > Wesley J?nio Alves da Concei??o
> > > Undergraduate Biophysics Student
> > > Laboratory for Molecular Modelling and Dynamics - Carlos Chagas Filho
> > > Biophysics Institute
> > > Laboratory for Structural Molecular Biology - Pharmacy Faculty
> > > Federal University of Rio de Janeiro
> > > Rio de Janeiro - RJ
> > > Brazil
> > > _______________________________________________
> > > 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 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Tue, 8 Mar 2016 07:31:40 +0000
> > From: <peter.schmidtke.discngine.servier.com>
> > Subject: Re: [AMBER] Gist calculation on clustered structures
> > To: <amber.ambermd.org>
> > Message-ID:
> > <D0B89EFF9EF07D4F87C038284FD89ADC3AA92CDD.CBSW2004.fr1.grs.net>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Cheers Steven,
> >
> > Thanks a lot for your answer!
> >
> > Peter
> >
> >
> > -----Message d'origine-----
> > De?: Steven Ramsey [mailto:vpsramsey.gmail.com]
> > Envoy??: mardi 1 mars 2016 15:30
> > ??: AMBER Mailing List
> > Objet?: Re: [AMBER] Gist calculation on clustered structures
> >
> > Hi Peter,
> >
> > You certainly can run GIST on a clustered trajectory and you should find
> > similar/ good convergence rates, it would depend on the number of frames
> in
> > your cluster, but my hunch on typical clustering protocols is that at
> least
> > your top cluster will perform well.
> >
> > The caveat is that sometimes structures that have been aligned lose
> system
> > information used in GIST energy calculations, producing strange
> > (arbitrarily high energy) results. Here's an archived response on the
> > matter: http://archive.ambermd.org/201508/0155.html .
> >
> > We're aware of this issue and working to fix it, the good news is that
> all
> > other terms calculated in GIST should behave normally on a clustered
> system.
> >
> > --Steve
> >
> >
> >
> > On Tue, Mar 1, 2016 at 2:23 AM, <peter.schmidtke.discngine.servier.com>
> > wrote:
> >
> > > Hello,
> > >
> > > I wondered if there is any literature or advice whether gist
> > > calculations could potentially be done on clustered conformations
> > > rather than fixed proteins and lengthy trajectories. Basically I have
> > > very long trajectories that I cluster around an area of interest and I
> > > end up with quite a large number of frames in a "stable" state.
> > > I guess the best way would be to check for convergence with this
> > > method versus a constrained trajectory, but I wanted to know if
> > > somebody actually did that already or not.
> > >
> > > Thanks in advance for your reply.
> > >
> > > Peter Schmidtke
> > > _______________________________________________
> > > 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: 4
> > Date: Tue, 8 Mar 2016 07:54:16 +0000 (UTC)
> > From: Saman Yousuf ali <saman.yousufali64.yahoo.com>
> > Subject: Re: [AMBER] cpptraj rmsd error (Orthogonal box), unknown
> > #frames, start=0 offset=1
> > To: Daniel Roe <daniel.r.roe.gmail.com>, AMBER Mailing List
> > <amber.ambermd.org>
> > Message-ID:
> > <1222914861.4384942.1457423656364.JavaMail.yahoo.mail.yahoo.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Dear Daniel,
> > Thank you for your help and guidance. I have decompressed these two
> > mdcrd.gz files. Its working fine.
> > Thanks??Best Regards,?Saman Yousuf AliJunior Research Fellow,
> > | Lab No. P-133, Computational Chemistry Laboratory
> > Dr. Panjwani Center for Molecular Medicine & Drug Research,
> > International Center for Chemical & Biological Sciences,
> > University of Karachi ? 75270.Karachi-Pakistan.
> >
> > Contact No:
> > Office (92-21) 111222292 (Ext 309)
> > Email ID:?saman.yousufali64.yahoo.com
> > saman.ali.iccs.edu
> >
> > ?? |
> >
> >
> >
> > On Monday, March 7, 2016 7:41 AM, Daniel Roe <daniel.r.roe.gmail.com
> >
> > wrote:
> >
> >
> > Hi,
> >
> > Likely your trajectory files 'md_simulation9.mdcrd.gz' and
> > 'md_simulation10.mdcrd.gz' have been either truncated or corrupted in
> > some way. If they are truncated, cpptraj may have a better chance of
> > reading the good frames if you first decompress (gunzip) the two
> > trajectories. If the corruption has happened in the middle of one or
> > both of the trajectories recovery of the data may not be possible. In
> > the future I recommend that you use the NetCDF trajectory and restart
> > formats (ioutfm=1 and ntxo=2 respectively) to avoid such issues.
> >
> > Hope this helps,
> >
> > -Dan
> >
> > On Sun, Mar 6, 2016 at 11:52 PM, Saman Yousuf ali
> > <saman.yousufali64.yahoo.com> wrote:
> > > I have performed 5 ns. I have run total 10 jobs, one job is equal to
> o.5
> > ns. After 4 ns (md run = 9) my was killed. I started again. When 5 ns
> > simultion completed, I have plotted rmsd graph using cpptraj.
> > > INPUT TRAJECTORIES:
> > >? 0: 'md_simulation1.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop
> > (Orthogonal box) (reading 2500 of 2500)
> > >? 1: 'md_simulation2.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop
> > (Orthogonal box) (reading 2500 of 2500)
> > >? 2: 'md_simulation3.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop
> > (Orthogonal box) (reading 2500 of 2500)
> > >? 3: 'md_simulation4.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop
> > (Orthogonal box) (reading 2500 of 2500)
> > >? 4: 'md_simulation5.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop
> > (Orthogonal box) (reading 2500 of 2500)
> > >? 5: 'md_simulation6.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop
> > (Orthogonal box) (reading 2500 of 2500)
> > >? 6: 'md_simulation7.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop
> > (Orthogonal box) (reading 2500 of 2500)
> > >? 7: 'md_simulation8.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop
> > (Orthogonal box) (reading 2500 of 2500)
> > >? 8: 'md_simulation9.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop
> > (Orthogonal box), unknown #frames, start=0 offset=1
> > >? 9: 'md_simulation10.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop
> > (Orthogonal box), unknown #frames, start=0 offset=1
> > >? Total number of frames is unknown.
> > > TIME: Run Initialization took 0.0015 seconds.
> > >
> > > BEGIN TRAJECTORY PROCESSING:
> > > .....................................................
> > >? In last two mdcrd.gz files number of frame is unknow, (Orthogonal
> box),
> > unknown #frames, start=0 offset=1). It effects rmsd plot.
> > >
> > >
> > >? ? ? ? Progress: '+' = 200 iterations.
> > > ----- md_simulation9.mdcrd.gz (1-EOF, 1) -----
> > >? ? ? ? ? 0
> > >? ? ? ? Progress: '+' = 200 iterations.
> > > ----- md_simulation10.mdcrd.gz (1-EOF, 1) -----
> > >
> > > I can not understand this error. Kindly help me in this regard.
> > > Thank you.
> > > Best Regards, Saman Yousuf AliJunior Research Fellow,
> > > | Lab No. P-133, Computational Chemistry Laboratory
> > > Dr. Panjwani Center for Molecular Medicine & Drug Research,
> > > International Center for Chemical & Biological Sciences,
> > > University of Karachi ? 75270.Karachi-Pakistan.
> > >
> > > Contact No:
> > > Office (92-21) 111222292 (Ext 309)
> > > Email ID: saman.yousufali64.yahoo.com
> > >? saman.ali.iccs.edu
> > >
> > >? ? |
> > >
> > > _______________________________________________
> > > 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 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Tue, 8 Mar 2016 10:36:47 +0000
> > From: Anna Cebrian Prats <Anna.Cebrian.uab.cat>
> > Subject: [AMBER] Chamber tool, error using the prmtop and inpcrd files
> > To: "amber.ambermd.org" <amber.ambermd.org>
> > Message-ID:
> > <
> >
> DBXPR07MB46105180889754A26EC5F7D8AB20.DBXPR07MB461.eurprd07.prod.outlook.com
> > >
> >
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hello,
> >
> >
> > I am working with a big molecule (5-LOX) that has a coordinate sphere
> with
> > a Fe (III).
> >
> >
> > I already have the .top, parm., psf and crd files in Charmm22 format. The
> > .top and .parm file where create by using Charmm- Gui.
> >
> >
> > For that reason, I used the chamber tool as this way;
> >
> >
> > chamber -cmap -top $PBS_O_WORKDIR/top_lox5.rtf -param \
> >
> > $PBS_O_WORKDIR/par_lox5.prm -psf $PBS_O_WORKDIR/pdb_lox5_wat.psf \
> >
> > -crd $PBS_O_WORKDIR/Lox5_wat.pdb -p 3o8y_w.prmtop -inpcrd 3o8y_w.inpcrd \
> > -box 90.0 95.0 93.0 -vmd -radius_set
> >
> >
> > And I obtain the added output file
> >
> >
> > It seems that the prmtop and inpcrd created are correct. Moreover, I
> > visualize the vmd_prmtop that I obtain and the coordinate sphere have the
> > correct interactions.
> >
> >
> > However, when I plot the minimization using the vmd_prmtop and the inpcrd
> > files, I obtain the following error.
> >
> >
> > - input file
> >
> >
> >
> > Minimization - protein and metal Fe+2
> > &cntrl
> > imin=1, maxcyc=200, ntpr=5,
> > &end
> >
> >
> > - Error
> >
> >
> >
> --------------------------------------------------------------------------------
> > 4. RESULTS
> >
> >
> --------------------------------------------------------------------------------
> >
> > ---------------------------------------------------
> > APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> > using 5000.0 points per unit in tabled values
> > TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> > | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> > | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
> > ---------------------------------------------------
> >
> > * NB pairs 416 52366507 exceeds capacity ( 52366666)
> > SIZE OF NONBOND LIST = 52366666
> > SANDER BOMB in subroutine nonbond_list
> > Non bond list overflow!
> > check MAXPR in locmem.f
> >
> >
> > Thank you in advanced for you help
> >
> >
> > Sincerely,
> >
> >
> > Anna Cebri?n
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Tue, 8 Mar 2016 08:09:08 -0500
> > From: Jason Swails <jason.swails.gmail.com>
> > Subject: Re: [AMBER] Chamber tool, error using the prmtop and inpcrd
> > files
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID: <32319CA8-289B-4160-8208-10601B5F11D0.gmail.com>
> > Content-Type: text/plain; charset=utf-8
> >
> > Try using pmemd instead of sander. Or run sander in serial.
> >
> > HTH,
> > Jason
> >
> > > On Mar 8, 2016, at 5:36 AM, Anna Cebrian Prats <Anna.Cebrian.uab.cat>
> > wrote:
> > >
> > > Hello,
> > >
> > >
> > > I am working with a big molecule (5-LOX) that has a coordinate sphere
> > with a Fe (III).
> > >
> > >
> > > I already have the .top, parm., psf and crd files in Charmm22 format.
> > The .top and .parm file where create by using Charmm- Gui.
> > >
> > >
> > > For that reason, I used the chamber tool as this way;
> > >
> > >
> > > chamber -cmap -top $PBS_O_WORKDIR/top_lox5.rtf -param \
> > >
> > > $PBS_O_WORKDIR/par_lox5.prm -psf $PBS_O_WORKDIR/pdb_lox5_wat.psf \
> > >
> > > -crd $PBS_O_WORKDIR/Lox5_wat.pdb -p 3o8y_w.prmtop -inpcrd 3o8y_w.inpcrd
> > \ -box 90.0 95.0 93.0 -vmd -radius_set
> > >
> > >
> > > And I obtain the added output file
> > >
> > >
> > > It seems that the prmtop and inpcrd created are correct. Moreover, I
> > visualize the vmd_prmtop that I obtain and the coordinate sphere have the
> > correct interactions.
> > >
> > >
> > > However, when I plot the minimization using the vmd_prmtop and the
> > inpcrd files, I obtain the following error.
> > >
> > >
> > > - input file
> > >
> > >
> > >
> > > Minimization - protein and metal Fe+2
> > > &cntrl
> > > imin=1, maxcyc=200, ntpr=5,
> > > &end
> > >
> > >
> > > - Error
> > >
> > >
> >
> --------------------------------------------------------------------------------
> > > 4. RESULTS
> > >
> >
> --------------------------------------------------------------------------------
> > >
> > > ---------------------------------------------------
> > > APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> > > using 5000.0 points per unit in tabled values
> > > TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> > > | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> > > | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
> > > ---------------------------------------------------
> > >
> > > * NB pairs 416 52366507 exceeds capacity ( 52366666)
> > > SIZE OF NONBOND LIST = 52366666
> > > SANDER BOMB in subroutine nonbond_list
> > > Non bond list overflow!
> > > check MAXPR in locmem.f
> > >
> > >
> > > Thank you in advanced for you help
> > >
> > >
> > > Sincerely,
> > >
> > >
> > > Anna Cebri?n
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > ------------------------------
> >
> > Message: 7
> > Date: Tue, 8 Mar 2016 15:34:48 +0100
> > From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
> > Subject: [AMBER] pseudo trajectories for 4 centers of mass?
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <
> > CAPKknGoW9PBqFhROnuN-sikc31+8YxE6FEOdJrFXFg8hOG5Q6w.mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi,
> >
> > Currently I am using vector command to save center of mass of one of the
> > sub-domain as:
> >
> > *vector S1 center :1-27,65-139.CA,C,N,O trajout S1.mdcrd parmout
> > vector.prmtop out rt-vector*
> >
> > But, my protein of interest consists 4 sub-domains and I need center of
> > mass of each subdomain..
> >
> > How can generate pseudo trajectories (and prmtop file) of all four COMs??
> >
> > Thanks,
> > Hirdesh
> > *?*
> >
> >
> > ------------------------------
> >
> > Message: 8
> > Date: Tue, 8 Mar 2016 08:02:38 -0700
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Subject: Re: [AMBER] pseudo trajectories for 4 centers of mass?
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <
> > CAAC0qOZcWzW1PRgYF8uCwM8q9B+PoKgsdBu8a+E648wLGCV2UQ.mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi,
> >
> > I responded to you regarding this a few days ago:
> > http://archive.ambermd.org/201603/0049.html
> >
> > Hopefully responses from the mailing list are reaching you.
> >
> > -Dan
> >
> > On Tue, Mar 8, 2016 at 7:34 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> > wrote:
> > > Hi,
> > >
> > > Currently I am using vector command to save center of mass of one of
> the
> > > sub-domain as:
> > >
> > > *vector S1 center :1-27,65-139.CA,C,N,O trajout S1.mdcrd parmout
> > > vector.prmtop out rt-vector*
> > >
> > > But, my protein of interest consists 4 sub-domains and I need center of
> > > mass of each subdomain..
> > >
> > > How can generate pseudo trajectories (and prmtop file) of all four
> COMs??
> > >
> > > Thanks,
> > > Hirdesh
> > > **
> > > _______________________________________________
> > > 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 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
> >
> >
> > ------------------------------
> >
> > Message: 9
> > Date: Tue, 08 Mar 2016 18:08:08 +0100
> > From: Zhang Marc <marczhang_md.zoho.com>
> > Subject: [AMBER] How to interpret MMGBSA ligand binding free energy
> > decomposition results
> > To: "amber" <amber.ambermd.org>
> > Message-ID: <15357333938.ea28cca8822.6592515782034870842.zoho.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> >
> >
> > Dear experts in Amber users group
> >
> >
> >
> > I performed a 20 ns MD simulations of a ligand-protein complex system.
> >
> >
> >
> > The ligand binding free energy was calculated using MMGBSA.
> >
> >
> >
> > The energy was decomposed onto residues in the binding pocket for
> > identifying residues important for ligand-protein interactions.
> >
> >
> >
> > Now I have difficulties to interpret the decomposition result, as it
> > suggested Threonine 119 is critical for both polar & non-polar
> > interactions.
> >
> >
> >
> > Here is the part of the result:
> >
> >
> >
> > Resides van der Waals Electrostatic Polar Solvation
> > Non-Polar Solvation TOTAL
> >
> > Thr119 -1.21 -2.37 0.27
> > -0.93 -4.23
> >
> >
> >
> > But Threonine is a polar residue and it is seldomly contributes to
> > hydrophobic interactions, as I was taught during biochemistry course.
> >
> >
> >
> > Could you please help me figure out where the problem is?
> >
> >
> >
> > Thanks a lot for your help!
> >
> >
> >
> > Cheers
> >
> > Marc
> >
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 10
> > Date: Tue, 8 Mar 2016 14:06:10 -0500
> > From: Arati Paudyal <apsilwal123.gmail.com>
> > Subject: [AMBER] Production phase for MMPBSA
> > To: AMBER Mailing List <amber.ambermd.org>
> > Message-ID:
> > <
> > CAJomNAgftaqPALEJw82UFskMYvJPCvZZAzM7SgbQoE2qid_4ow.mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear all,
> >
> > I just finished the tutorial for MMPB/GB SA with ras-raf protein and I
> > followed the tutorial. But this time I ran the the equilibrium step for
> > 30,000,000 steps for a total simulation time of 60 ns instead of 500 ps
> as
> > in tutorial. In the tutorial, there are separate production steps run
> for a
> > total of 2 ns. I guess, my questions is, if you run your equilibiation
> > phase for 60 ps already, do I need to run the production step again? I
> > checked everything including rmsd, energy and density and my system is
> > fully equilibriated.
> >
> > If NOT, then when we run the mmpbsa.py script, how do we start from the
> > point where the system is already equilibriated? Is it something do do
> with
> > the start and end frames in the script? For eg. following is the rmsd
> plot
> > of my system afte 60ns of equilibriation. I can see the system is
> > equilibriated after about 200 frames. So can I assign my start frame as
> 200
> > and end frame as 700?
> >
> > Sorry to put up these simple questions but if anybody could give some
> > response/suggestions, it would be really helpful.
> >
> > (First few frames)
> >
> > #Frame RMSD_00001
> > 0.2 0.6366
> > 0.4 0.6494
> > 0.6 0.6472
> > 0.8 0.6625
> > 1 0.6608
> > 1.2 0.665
> >
> > [image: Inline image 1]
> >
> >
> >
> >
> >
> >
> > Thanks in advance for your valuable time.
> > -------------- next part --------------
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> >
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> >
> > ------------------------------
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > End of AMBER Digest, Vol 1509, Issue 1
> > **************************************
> >
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Received on Tue Mar 08 2016 - 22:00:03 PST
