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 <
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> 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.
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> End of AMBER Digest, Vol 1509, Issue 1
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Received on Tue Mar 08 2016 - 20:30:05 PST
