I have done protein-protein simulation studies and I am stuck in the
secondary structure analysis. In this regard, I need a little guidance
about plotting graph for secondary structure. I have used amber for
simulation and perform secondary structure analysis by cpptraj command i.e.
*secstruct : 1-336 out dssp.gnu sumout dssp.agr.sum*
Now problem is that I am unable to plot the generated files. It is not
plotted correctly by gnuplot or xmgrace or may be I don't know the commands
for plotting.Can you please tell me the procedure or commands for these
files.Apart of it, I have also generated files by DSSP software which
generated output files having .dssp extension and similarly I could not
understand how to plot this file because there is no such software which
plot or read these generated files and I am unable to find any script for
plotting this file.So please guide me in this regard.
*Regards,*
* Sehrish Naz*
*Jr. Research Fellow,*
*Computational Chemistry Unit.*
*Dr. Panjwani Center for Molecular Medicine and Drug Research,*
*International Center for Chemical and Biological Sciences,*
*University of Karachi, Karachi-75270.*
*E-mail: mjazse.gmail.com <misbah.anwar88.gmail.com>*
On Wed, Sep 16, 2015 at 12:00 AM, <amber-request.ambermd.org> wrote:
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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: Proper Insertion of Covalently Bound Unit in Helical
> Structure (Robert Molt)
> 2. Re: MCPB problem (Pengfei Li)
> 3. Re: What is wrong with the minimization? (David A Case)
> 4. Re: Paramfit issues (Robin Betz)
> 5. Re: Proper Insertion of Covalently Bound Unit in Helical
> Structure (David A Case)
> 6. mmpbsa error (Lara rajam)
> 7. Regarding Simulations of Ionic Liquids on GPU
> (MOHD HOMAIDUR RAHMAN)
> 8. A question on binding free energy decomposition output (wliu)
> 9. Re: A question on binding free energy decomposition output
> (Sofia Vasilakaki)
> 10. Re: Regarding Simulations of Ionic Liquids on GPU (David A Case)
> 11. query (ankita mehta)
> 12. query (Kenneth Huang)
> 13. sqm (Sofia Vasilakaki)
> 14. Re: sqm (Hannes Loeffler)
> 15. Re: mmpbsa error (Jason Swails)
> 16. Re: sqm (Sofia Vasilakaki)
> 17. Re: A question on binding free energy decomposition output
> (Jason Swails)
> 18. Re: sqm (Jason Swails)
> 19. Re: sqm (Hannes Loeffler)
> 20. Has anyone tried VMD in the second step of tutorial A1? (Xing)
> 21. vlimit exceeded and high temperature (Ruth Helena Tichauer)
> 22. Re: mmpbsa error (Lara rajam)
> 23. cyclic peptides and bond command in leap (Jonathan Gough)
> 24. Re: mmpbsa error (Jason Swails)
> 25. Re: query (David A Case)
> 26. Re: sqm (David A Case)
> 27. Antechamber error (Kalenkiewicz, Andrew (NIH/NICHD) [F])
> 28. Re: vlimit exceeded and high temperature (David A Case)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 14 Sep 2015 16:58:22 -0400
> From: Robert Molt <rwmolt07.gmail.com>
> Subject: Re: [AMBER] Proper Insertion of Covalently Bound Unit in
> Helical Structure
> To: david.case.rutgers.edu, AMBER Mailing List <amber.ambermd.org>
> Message-ID: <55F734EE.1080901.gmail.com>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Ah...I am quite dense. "DU" is no doubt dummy. Sorry I did not see this
> sooner.
>
> Nonetheless, I am still confused on how to proceed. If the Amber FF
> types do not include all the ones in GAFF, what is the right procedure?
>
> On 9/14/15 12:01 AM, David A Case wrote:
> > On Sun, Sep 13, 2015, Robert Molt wrote:
> >> I am having difficulty inserting a covalently bound unit within a DNA
> >> helix (it is internal, not terminal).
> >>
> >> 2.) I do not believe that this is an option for me; there are "missing
> >> parameters" using "amber" force fields (the GAFF parameters are complete
> >> when I check them). Can this advice be modified for using a nucleotide
> >> with purely GAFF generated parameters?
> > You can, but then there will be missing parameters at the intersection
> between
> > the modified nucleotide (which has gaff atom types), and the regular
> > nucleotides (which will have Amber atom types).
> >
> > I recommed that you run antechamber twice, once with Amber atom types
> and once
> > with gaff. Use the gaff results to fill in the missing parameters in the
> > Amber atom type result. (You'll have to do this by hand, by editing the
> > frcmod file). Then use the Amber atom type unit.
> >
> >> 3.) I have thus tried to create a new unit based on the advice on
> >> creating a new unit, but failed. I think this is because I do not
> >> understand why one cannot simply
> >>
> >> UNIT_NAME=loadmol2 NAME.mol2
> >> loadamberparams NAME.frcmod
> > You can do this. Just saying the "it failed" (or "it fails terribly")
> > doesn't give us anything to go on in terms making suggestions.
> >
> >> and make sure the pdb name matches NAME for the unit? This fails
> >> terribly, but I do not understand why (because I am not really sure I
> >> understand how leap "recognizes" units and adds in the "right" missing
> >> atoms (like a terminal P or O in a helix, or a missing hydrogen). I get
> >> atoms overlapping ontop of one another.
> > Once you load the units (as above), you can use the "desc" command in
> LEaP
> > to find out what LEaP thinks the residue name and atom names are in the
> unit
> > you loaded. You have to make sure that the residue and atom names in
> the pdb
> > file match those you get from the "desc" command.
> >
> > If there are atoms in the library but which are missing from the pdb
> file,
> > LEaP will try to build them in. The other mismatch (where you have atoms
> > in the pdb file that are missing in the library) is almost always a fatal
> > error. From the very brief account you have given, I'm guessing that the
> > atom names in your pdb file don't match those in the NAME.mol2 file.
> >
> >
> >> 4.) I do apologize if this information is in the Amber tutorials; to my
> >> knowledge, 2 of them deal with non-connected ligand parameterization,
> >> and one deals with connected-non-standard residue insertion in a protein
> >> (whose process seems very different than for a helix).
> >>
> > Tutorial B5 is the one that is closest to what you are doing. There is
> no
> > fundamental different in procedure between modified amino acids and
> modified
> > nucleotides.
> >
> > ...good luck....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Robert Molt Jr.
> r.molt.chemical.physics.gmail.com
> Visiting Associate Professor of Chemistry
> Department of Chemistry & Chemical Biology
> Indiana University-Purdue University Indianapolis
> LD 326
> 402 N. Blackford St.
> Indianapolis, IN 46202
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 14 Sep 2015 17:28:42 -0400
> From: Pengfei Li <ambermailpengfei.gmail.com>
> Subject: Re: [AMBER] MCPB problem
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <3E9D6565-CB6D-4853-98B2-7C1A46B1D102.gmail.com>
> Content-Type: text/plain; charset=utf-8
>
> Hi Kshatrech,
>
> Can you send me the input file and PDB file about your system in an
> private email? I can do a check about what is wrong.
>
> > On Sep 14, 2015, at 1:42 PM, Kshatresh Dutta Dubey <kshatresh.gmail.com>
> wrote:
> >
> > Hi Pengfei,
> >
> > Thanks for reply. Yes, both have the same atom and residue name in mol2
> and
> > pdb files. However, it is successfully generating all necessary
> files(side
> > chain model, standard model and large model) but the name of 'Fe' atom in
> > Gaussian input is 'F' (which is for fluorine ). I followed your previous
> > post
> >
> > http://archive.ambermd.org/201505/0351.html <
> http://archive.ambermd.org/201505/0351.html>
> >
> > where similar error was reported. As per your suggestion, changing atom
> > name and residue name as FE2, gives new error : key error: FE2-FE2 and
> in
> > this case necessary files for large model is not generated. Therefore, I
> > followed the previous step where atom name is FE and residue name is FE2
> > and I manually renamed F of Gaussian file as Fe and ran the optimization.
> > Please suggest me whether these files are okay to proceed for the next
> > stage of parameterization. I would be very thankful for your help.
> >
>
> It should be careful about this situation due to it seems MCPB.py did not
> treat Fe ion as it should be. This problem may cause trouble in the later
> steps.
>
> Best,
> Pengfei
>
> > Best regards
> > Kshatresh
> >
> > On Mon, Sep 14, 2015 at 7:15 PM, Pengfei Li <ambermailpengfei.gmail.com
> <mailto:ambermailpengfei.gmail.com>>
> > wrote:
> >
> >> Hi Kshatresh,
> >>
> >>> Hi Pengfei,
> >>>
> >>> Sorry for multiple posting. I recompiled the MCPB program after
> >> installing
> >>> scipy and this fixes the program error. Many thanks for your help.
> >>
> >> No problem.
> >>
> >>> However,
> >>> it is showing error while running the my input as follows but gives all
> >>> necessarily files eg gaussian inputs for side chain and large model,
> >>> fingerprint files etc.
> >>> .......
> >>> ......
> >>> Creating the normal residue 387-S0H
> >>> Totally there are 106 atoms in the large model.
> >>> Totally there are 457 electrons in the large model.
> >>> Traceback (most recent call last):
> >>> File "/usr/local/amber14/bin/MCPB.py", line 419, in <module>
> >>> watermodel, 2, sqmopt)
> >>> File
> >>>
> >>
> "/usr/local/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> >>> line 1167, in gene_model_files
> >>> ionids, chargedict, totchg, outf, watermodel, sqmopt)
> >>> File
> >>>
> >>
> "/usr/local/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> >>> line 984, in build_large_model
> >>> chg = str(int(chargedict[i]))
> >>> KeyError: ?FE'
> >>>
> >>
> >> Is the Fe ion in the FE.mol2 file has the same residue and atom names as
> >> it in the PDB file (e.g. all have ?FE" as residue name and as atom
> name)?
> >>
> >>>
> >>> I followed the same input as in MCPB tutorial, changed the atom id for
> FE
> >>> according to pdb, produced WAT.mol2 files. However I am not sure how to
> >> add
> >>> WAT.mol2 file in input and there is no information about this in manual
> >> as
> >>> well. In addition I found that program MCPB assigns FE as Z1 in
> >> fingerprint
> >>> file generated by run.
> >>
> >> You can add WAT.mol2 file name after the naa_mol2files variable in the
> >> MCPB.py input file, it is fine for naa_mol2files variable following by
> >> several mol2 file names.
> >>
> >> MCPB.py will assign FE as Z1 automatically during the parameterization
> >> step if you pick the default mode for step 1, which will make the Fe ion
> >> has a unique atom type from other atoms. It is fine.
> >>
> >>>
> >>> Please help me regarding these issues. Thanks in advance.
> >>>
> >>
> >> Best,
> >> Pengfei
> >>
> >>> On Sun, Sep 13, 2015 at 5:11 AM, Kshatresh Dutta Dubey <
> >> kshatresh.gmail.com <mailto:kshatresh.gmail.com> <mailto:
> kshatresh.gmail.com <mailto:kshatresh.gmail.com>>>
> >>> wrote:
> >>>
> >>>> Hi,
> >>>>
> >>>> Thanks for help. I found that python-scipy was not installed. I
> >> installed
> >>>> scipy but still I am facing some problem and now the error is :
> >>>> Traceback (most recent call last):
> >>>> File "/usr/local/amber14/bin/MCPB.py", line 46, in <module>
> >>>> from mcpb.gene_model_files import get_ms_resnames, gene_model_files
> >>>> ImportError: No module named mcpb.gene_model_files
> >>>>
> >>>> Please help me the to fix this issue.
> >>>>
> >>>> On Sun, Sep 13, 2015 at 2:30 AM, Pengfei Li <
> ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>
> >>>
> >>>> wrote:
> >>>>
> >>>>> Hi Kshatresh,
> >>>>>
> >>>>> It seems the error implies that you did not install scipy in the
> >> machine.
> >>>>> Can you do a quick check by using the following command *python -c
> >> "import
> >>>>> scipy"*, if there is error raised, which means you did not install
> >> scipy
> >>>>> indeed.
> >>>>>
> >>>>> Best,
> >>>>> Pengfei
> >>>>>
> >>>>> 2015-09-12 10:45 GMT-04:00 Kshatresh Dutta Dubey <
> kshatresh.gmail.com <mailto:kshatresh.gmail.com>
> >>> :
> >>>>>
> >>>>>> HI Pengfei,
> >>>>>>
> >>>>>> I am facing a new problem during MCPB.py run after installing
> >> AmberTool
> >>>>> 15.
> >>>>>> It seems to me something is wrong with python interpreter, but
> other
> >>>>>> programs like MMPBSA.py is running fine with same installations. I
> >> have
> >>>>>> correctly defined the python environment as it is mentioned in
> >>>>> amber.sh. I
> >>>>>> am getting following error during MCPB.py :
> >>>>>>
> >>>>>> Traceback (most recent call last):
> >>>>>> File "/usr/local/amber14/bin/MCPB.py", line 46, in <module>
> >>>>>> from mcpb.gene_model_files import get_ms_resnames,
> gene_model_files
> >>>>>> File
> >>>>>>
> >>>>>
> >>
> "/usr/local/amber14/lib/python2.7/site-packages/mcpb/gene_model_files.py",
> >>>>>> line 13, in <module>
> >>>>>> from pymsmtlib.lib import get_lib_dict
> >>>>>> File
> >>>>> "/usr/local/amber14/lib/python2.7/site-packages/pymsmtlib/lib.py",
> >>>>>> line 8, in <module>
> >>>>>> from scipy.optimize import curve_fit
> >>>>>> ImportError: No module named scipy.optimize
> >>>>>>
> >>>>>> Please help me to figure out the problem.
> >>>>>>
> >>>>>> Thanking you
> >>>>>> Kshatresh
> >>>>>>
> >>>>>>
> >>>>>> On Fri, Sep 11, 2015 at 7:19 PM, Pengfei Li <
> >> ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>
> >>>>>>
> >>>>>> wrote:
> >>>>>>
> >>>>>>> Hi Kshatresh,
> >>>>>>>
> >>>>>>> It also supports Zn. The following words in the tutorial may be
> >>>>>> confusing:
> >>>>>>>
> >>>>>>> Z-matrix methodThe bond and angle force constants are determined
> from
> >>>>> the
> >>>>>>> Cartesian Hessian matrixSeminario MethodThe bond and angle force
> >>>>>> constants
> >>>>>>> are determined from the sub matrices of the Cartesian Hessian
> >>>>>>> matrixEmpirical
> >>>>>>> Method (Only in MCPB.py)The bond and angle force constants are
> >>>>> determined
> >>>>>>> from an empirical method developed by Li et al. in Merz Research
> >>>>> Group,
> >>>>>>> current version only supports bonded model of Zinc ion
> >>>>>>>
> >>>>>>> Actually it means, MCPB supports two methods (Z-matrix and
> >> Seminario),
> >>>>>>> while MCPB.py supports three methods (Z-matrix, Seminario and an
> >>>>>> empirical
> >>>>>>> one). The empirical method in MCPB.py only supports Zn ion now but
> >> for
> >>>>>> the
> >>>>>>> other two methods in MCPB.py they support a lot of ions.
> >>>>>>>
> >>>>>>> Best,
> >>>>>>> Pengfei
> >>>>>>>
> >>>>>>> 2015-09-11 12:15 GMT-04:00 Kshatresh Dutta Dubey <
> >> kshatresh.gmail.com <mailto:kshatresh.gmail.com>
> >>>>>> :
> >>>>>>>
> >>>>>>>> Hi Pengfei
> >>>>>>>>
> >>>>>>>> Thanks for your reply. Does the python version also support for
> Fe?
> >>>>>> Some
> >>>>>>>> time ago I read that present version supports only for Zn.
> >>>>>>>>
> >>>>>>>> On Fri, Sep 11, 2015 at 6:56 PM, Pengfei Li <
> >>>>>> ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>>
> >>>>>>>> wrote:
> >>>>>>>>
> >>>>>>>>> Dear Kshatresh,
> >>>>>>>>>
> >>>>>>>>> There is a program called MCPB.py, a python substitute of MCPB,
> in
> >>>>>>>>> AmberTools15 (AmberTools15 is free and you can download it here:
> >>>>>>>>> http://ambermd.org/AmberTools15-get.html). It takes much less
> >>>>> time
> >>>>>> to
> >>>>>>>>> parameterize a metal site by using MCPB.py than MCPB. There is
> >>>>> also a
> >>>>>>> web
> >>>>>>>>> tutorial about MCPB.py:
> >>>>>>>>> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm. If
> >>>>> you
> >>>>>>> have
> >>>>>>>>> more questions, please feel free to email me.
> >>>>>>>>>
> >>>>>>>>> Best,
> >>>>>>>>> Pengfei
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> 2015-09-10 16:25 GMT-04:00 Kshatresh Dutta Dubey <
> >>>>>> kshatresh.gmail.com
> >>>>>>>> :
> >>>>>>>>>
> >>>>>>>>>> Dear Users,
> >>>>>>>>>>
> >>>>>>>>>> I am using MCPB for building parameter of iron containing
> >>>>> protein.
> >>>>>> I
> >>>>>>> am
> >>>>>>>>>> following exactly the same steps as described in MCPB tutorial,
> >>>>>>>> however I
> >>>>>>>>>> am getting problem in copying StdResidue in during
> >>>>> _sidechain.bcl,
> >>>>>>>>>> particularly to the line describing metal (FE). I am
> >>>>> attaching my
> >>>>>>>>>> _sidechain.bcl as well as pdb file.
> >>>>>>>>>> Please help me to fix this problem
> >>>>>>>>>>
> >>>>>>>>>> --
> >>>>>>>>>> With best regards
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>
> >>
> ************************************************************************************************
> >>>>>>>>>> Kshatresh Dutta Dubey
> >>>>>>>>>> Post Doctoral Researcher,
> >>>>>>>>>> Lise Meitner Center for Computational Quantum Chemistry
> >>>>>>>>>> Hebrew University of Jerusalem Israel
> >>>>>>>>>> Jerusalem, Israel
> >>>>>>>>>>
> >>>>>>>>>> _______________________________________________
> >>>>>>>>>> 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
> >>>>>>>>> _______________________________________________
> >>>>>>>>> AMBER mailing list
> >>>>>>>>> AMBER.ambermd.org
> >>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> --
> >>>>>>>> With best regards
> >>>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>
> >>
> ************************************************************************************************
> >>>>>>>> Kshatresh Dutta Dubey
> >>>>>>>> Post Doctoral Researcher,
> >>>>>>>> Lise Meitner Center for Computational Quantum Chemistry
> >>>>>>>> Hebrew University of Jerusalem Israel
> >>>>>>>> Jerusalem, Israel
> >>>>>>>> _______________________________________________
> >>>>>>>> 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
> >>>>>>> _______________________________________________
> >>>>>>> AMBER mailing list
> >>>>>>> AMBER.ambermd.org
> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> With best regards
> >>>>>>
> >>>>>>
> >>>>>
> >>
> ************************************************************************************************
> >>>>>> Kshatresh Dutta Dubey
> >>>>>> Post Doctoral Researcher,
> >>>>>> Lise Meitner Center for Computational Quantum Chemistry
> >>>>>> Hebrew University of Jerusalem Israel
> >>>>>> Jerusalem, Israel
> >>>>>> _______________________________________________
> >>>>>> 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
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> With best regards
> >>>>
> >>>>
> >>
> ************************************************************************************************
> >>>> Kshatresh Dutta Dubey
> >>>> Post Doctoral Researcher,
> >>>> Lise Meitner Center for Computational Quantum Chemistry
> >>>> Hebrew University of Jerusalem Israel
> >>>> Jerusalem, Israel
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>> --
> >>> With best regards
> >>>
> >>
> ************************************************************************************************
> >>> Kshatresh Dutta Dubey
> >>> Post Doctoral Researcher,
> >>> Lise Meitner Center for Computational Quantum Chemistry
> >>> Hebrew University of Jerusalem Israel
> >>> Jerusalem, Israel
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org <mailto:AMBER.ambermd.org> <mailto:AMBER.ambermd.org
> <mailto:AMBER.ambermd.org>>
> >>> http://lists.ambermd.org/mailman/listinfo/amber <
> http://lists.ambermd.org/mailman/listinfo/amber> <
> >> http://lists.ambermd.org/mailman/listinfo/amber <
> http://lists.ambermd.org/mailman/listinfo/amber>>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> >> http://lists.ambermd.org/mailman/listinfo/amber <
> http://lists.ambermd.org/mailman/listinfo/amber>
> >>
> >
> >
> >
> > --
> > With best regards
> >
> ************************************************************************************************
> > Kshatresh Dutta Dubey
> > Post Doctoral Researcher,
> > Lise Meitner Center for Computational Quantum Chemistry
> > Hebrew University of Jerusalem Israel
> > Jerusalem, Israel
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> > http://lists.ambermd.org/mailman/listinfo/amber <
> http://lists.ambermd.org/mailman/listinfo/amber>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 14 Sep 2015 17:40:47 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] What is wrong with the minimization?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20150914214047.GH55383.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Mon, Sep 14, 2015, Huggins, Esther, C wrote:
>
> > I have a minimization run previous to this, and I set up the ipol to a
> > default 1. So how should I equilibrate the system with non polirizable
> > potentials? How much is minimized?
> >
> > The minimization is now resulting in this
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 50 -2.8320E+05 2.3084E+06 3.2614E+07 HW 112
> >
> > BOND = 0.0043 ANGLE = 0.0113 DIHED =
> 0.0000
> > VDWAALS = 14.4210 EEL = 3141.9935 HBOND =
> 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
> > EPOLAR = -286353.0043
> > Dipole convergence: rms = 0.455E+04 temperature = 0.00
>
> Something is dreadfully wrong here. Your dipole convergence should on the
> order of 1.e-5, not 1.e+4. The RMS gradient is enormous...it looks like
> you
> may have hit a "polarization catastrophe." How did you set up your system?
> What potentials are you using?
>
> Note that Amber has not been used a lot for simulations with polarizable
> potentials, and the potentials using polarizability have not been updated
> for
> a long time. So there may be cases that don't work all that well. If you
> really need polarizable potentials, you will need to provide more details
> about how you prepared the system.
>
> .....dac
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 14 Sep 2015 14:53:44 -0700
> From: Robin Betz <robin.robinbetz.com>
> Subject: Re: [AMBER] Paramfit issues
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAL9_cpdR9Xn7Yfk=
> M9yx-uZqA9oFn2x2ig2BLEf5sKrk8ChUYA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi David,
> I've responded to your questions inline:
>
> On Mon, Sep 14, 2015 at 3:31 AM, David Poole <thepoole.ucdavis.edu> wrote:
>
> > Hello Everybody,
> >
> > I'd been continuing my effort to produce some specialized heme parameters
> > and decided that it might be the simplest to use paramfit and a large
> > number of QM derived structures+energies. But after the QM is done, I've
> > questions.
> >
> >
> > 1) During the optimization process Gaussian produces a number of
> structures
> > with energies that are sub-optimal configurations, is there any reason
> why
> > these cannot or should not be used for parameter fitting? or other
> concerns
> > in that regard?
> >
>
> Paramfit doesn't know anything about the underlying chemistry or dynamics
> the parameters are supposed to accurately describe. All it can do is fit an
> energy function as best as it can. So, if non-representative conformations
> are input, it will do its best to get parameters that describe those
> conformations, which can result in poor description of actually relevant
> regions of conformation space that are sampled during simulation.
>
> If you think the conformations are sub-optimal, you can weight them so that
> they are less important to the fitting algorithm. See this section of the
> tutorial for how high-energy / bad conformers can bias a fit and how to
> weight them less for better parameters overall:
> http://ambermd.org/tutorials/advanced/tutorial23/paramfit_5.html
>
> >
> > 2) Is there a way to run paramfit on multiple processors?
> >
>
> Paramfit can use OpenMP to parallelize the energy calculation across
> available CPU cores. You need to
> configure AmberTools with OpenMP support (./configure -openmp) and
> recompile. Use the OMP_NUM_THREADS environment variable to configure how
> many cores to use, with all being used by default. Look for a line near the
> beginning of program output stating OpenMP is being used.
>
> >
> > 3) I derived the correction constant K using the method described in the
> > tutorial, and then ran it to find parameters by list as well as the
> default
> > (since I want to optimize all parameters), in both circumstances it set
> the
> > initial value of K to zero, this obviously deviates from the output files
> > in the tutorial.. so I probably need help with this.
> >
>
> That is most likely a bug that I have since fixed. Are you on the latest
> version of AmberTools with all available patches?
>
>
> > 4) I am getting some warning related to dihedral spans lacking data
> > coverage, given that Is fitting dehedral parameters to the heme system
> > unnecessary or is this not a significant message?
> >
>
> Given the bond and angle constraints present on the heme group I wouldn't
> worry about sampling with those dihedrals as those bonds are not rotatable.
>
> >
> > 5) Any other pointers would be greatly appreciated.
> >
> > If you are performing the fit on iron heme, be very careful with your
> quantum calculations as it can be tricky to accurately characterize the
> iron atom's spin state. You will probably have to pick whichever state
> predominates in your system of interest, or fit bonded parameters for zinc
> heme. Have you seen these parameters for P450 heme?
> http://www.ncbi.nlm.nih.gov/pubmed/15812779
>
> Best,
> Robin Betz
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 14 Sep 2015 18:04:13 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Proper Insertion of Covalently Bound Unit in
> Helical Structure
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20150914220413.GO55383.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Mon, Sep 14, 2015, Dr. Robert Molt Jr. wrote:
> >
> > 1.) The reason the process of covalent unit creation in a helix is
> > seemingly different (at least to my naive eye) compared to the tutorial
> > on proteins is the linkage. I know how amino acids link internally;
> > there is only one way to do it (NHCO formation). I am confused on a
> > helix because I am unsure what unit Leap will look for: nucleic acid,
> > nucleotide, nucleoside?
>
> Think of LEaP as a bookkeeiping program: it doesn't whether it is dealing
> with
> a protein, a nucleic acid, or anything else. It doesn't know the
> difference
> between a nucleotide, nucleoside, etc.
>
> Here's what it does: it looks at the residue names in your input pdb file,
> and
> tries to match that against the list of units it knows about (which you can
> see using the "list" command). When it finds a match, it lines up the
> atoms
> in the pdb with those in the library unit. The *only* time it will try to
> "build" the location of atoms is if there are atoms in the library that are
> missing in the pdb file. It uses the head and tail atom designations in
> the
> library to decide how (if at all) to covalently bond one residue to the
> next
> one.
>
> `
> > but I am unsure what atoms Leap will automatically assume to add
> > in to connect.
>
> Hope the above makes this clear: it has nothing to do with chemistry. It
> will
> only "add" atoms if they are in the residue library but are missing in the
> pdb
> file.
>
> >
> > 2.) Using just a nucleic acid as the parameterized units...
> >
> > I understand that most atom types differ only by case (upper/lower)
> > between GAFF/Amber style text formatting. However, I am seeing atom
> > types in the amber parameterization that I cannot identify. For example:
> >
> > MASS
> > CA 12.010 0.360 same as c2
> > C 12.010 0.616 same as c
> > HA 1.008 0.135 same as hc
> > O 16.000 0.434 same as o
> > NA 14.010 0.530 same as na
> > H 1.008 0.161 same as hn
> > N2 14.010 0.530 same as n3
> > NO 0.000 0.000 ATTN, need revision
> > DU 0.000 0.000 ATTN, need revision
> >
> > includes "DU," which I do not know how to identify. This does not seem
> > to be a standard Amber designation of an atom, based on what I google
> > searched or in the manual? I am guessing I did not ask for Amber
> > parameters properly:
>
> DU stands for "dummy": something must have gone rather wrong in running
> antechamber. You may need to post the "File.pdb" file you used to get this
> example.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 14 Sep 2015 21:40:49 -0400
> From: Lara rajam <lara.4884.gmail.com>
> Subject: [AMBER] mmpbsa error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAPQ+66D0HMBZqcXfzPV-ByH5yP77o1bE2=jbN1i8pv+=
> dDjFHg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Amber
>
> I am trying to do the MMPBSA calculation , earlier I was generating the
> parameters with ff99SB and I was able to run mmpbsa.py
>
> Now I generated the prmtop using ff12SB , I was not able to run mmpbsa
> calculation, the error is as below I am running in serial mode. I again
> generated all the prmtop and did a try, the error is the same and my input
> is below
>
> INPUT file
>
> Input file for running PB and GB in serial
>
> &general
>
> endframe=50, keep_files=2,
>
> /
>
> &gb
>
> igb=2, saltcon=0.100,
>
> /
>
> &pb
>
> istrng=0.100,
>
> /
>
>
> OUT PUT ERROR !
>
> [TEST.NEMO dr2]$ $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o
> FINAL_RESULTS_MMPBSA.dat -sp solvated_di.prmtop -cp complex.prmtop -rp
> protein.prmtop -lp ligand.prmtop -y *.mdcrd
>
> Loading and checking parameter files for compatibility...
>
> mmpbsa_py_energy found! Using
> /home/TEST/AMBERHOME/amber14/bin/mmpbsa_py_energy
>
> cpptraj found! Using /home/TEST/AMBERHOME/amber14/bin/cpptraj
>
> Preparing trajectories for simulation...
>
> 50 frames were processed by cpptraj for use in calculation.
>
>
> Running calculations on normal system...
>
>
> Beginning GB calculations with
> /home/TEST/AMBERHOME/amber14/bin/mmpbsa_py_energy
>
> calculating complex contribution...
>
> File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA.py", line 96, in ?
>
> app.run_mmpbsa()
>
> File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA_mods/main.py", line 218, in
> run_mmpbsa
>
> self.calc_list.run(rank, self.stdout)
>
> File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA_mods/calculation.py", line
> 79, in run
>
> calc.run(rank, stdout=stdout, stderr=stderr)
>
> File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA_mods/calculation.py", line
> 147, in run
>
> raise CalcError('%s failed with prmtop %s!' % (self.program,
>
> CalcError: /home/TEST/AMBERHOME/amber14/bin/mmpbsa_py_energy failed with
> prmtop complex.prmtop!
>
> Exiting. All files have been retained.
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 15 Sep 2015 11:15:41 +0530
> From: MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>
> Subject: [AMBER] Regarding Simulations of Ionic Liquids on GPU
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAPyy0JxOisuxD3eshNFdUJ5W8YVBWwyXPp2CfRUUaiUGL13K6w.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Amber Users
>
> I have a system that contains Ionic Liquids ( organic cation and inorganic
> anion ) and we are simulating this systems by using Sander module with full
> ewald (by EW_TYPE=1 keyword). The GPU version of simulation module PMEMD is
> not supporting the full ewald method.
>
> So my question is that the scientific community accepting this type of
> systems simulated on pmemd (GPU). And what is the best way to simulate this
> type of systems.
>
> Thanks & regards
> Rahman
>
>
> ------------------------------
>
> Message: 8
> Date: Tue, 15 Sep 2015 14:22:27 +0800
> From: wliu <wliu.itcs.ecnu.edu.cn>
> Subject: [AMBER] A question on binding free energy decomposition
> output
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <bb7d71617a8d3cfac24887e44dcdc372.itcs.ecnu.edu.cn>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Dear all,
>
> I have a simple question about the output of binding free energy
> decomposition. I calculated Per-residue energy decomposition for
> specific residues with mmpbsa.py and I got the FINAL_DECOMP_MMPBSA.dat
> file.
>
> DELTAS:
> Total Energy Decomposition:
> Residue | Location | Internal | van der Waals |
> Electrostatic | Polar Solvation | Non-Polar Solv. |
> TOTAL
>
> -------------------------------------------------------------------------------------------------------------------------------------------------------
> LEU 18 | R LEU 18 | 0.000 +/- 0.000 | -2.968 +/- 0.505 |
> -0.436 +/- 0.232 | 3.215 +/- 0.453 | 0.000 +/- 0.000 | -0.189
> +/- 0.583
> GLU 20 | R GLU 20 | 0.000 +/- 0.000 | -1.521 +/- 0.431 |
> -0.527 +/- 1.684 | 0.859 +/- 1.585 | 0.000 +/- 0.000 | -1.189
> +/- 0.539
>
> Then here is my question, Does the value after +/- sign stand for
> standard deviation of the calculated energy, or standard error instead?
>
> Thanks & regards
> Wei Liu
>
>
>
> ------------------------------
>
> Message: 9
> Date: Tue, 15 Sep 2015 11:01:20 +0300
> From: "Sofia Vasilakaki" <svasilak.chem.uoa.gr>
> Subject: Re: [AMBER] A question on binding free energy decomposition
> output
> To: "AMBER Mailing List" <amber.ambermd.org>
> Message-ID:
> <8008af8a886d8bd5528a41fdfa63ff79.squirrel.webmail01.uoa.gr>
> Content-Type: text/plain;charset=utf-8
>
> Actually, it would be useful if someone could explain a bit the
> Decomposition output. What kind of info you get by knowing the energy
> values for each residue, especially for those in the active site?
>
> Thank you,
> Sofia V.
>
>
>
>
> > Dear all,
> >
> > I have a simple question about the output of binding free energy
> > decomposition. I calculated Per-residue energy decomposition for
> > specific residues with mmpbsa.py and I got the FINAL_DECOMP_MMPBSA.dat
> > file.
> >
> > DELTAS:
> > Total Energy Decomposition:
> > Residue | Location | Internal | van der Waals |
> > Electrostatic | Polar Solvation | Non-Polar Solv. |
> > TOTAL
> >
> -------------------------------------------------------------------------------------------------------------------------------------------------------
> > LEU 18 | R LEU 18 | 0.000 +/- 0.000 | -2.968 +/- 0.505 |
> > -0.436 +/- 0.232 | 3.215 +/- 0.453 | 0.000 +/- 0.000 | -0.189
> > +/- 0.583
> > GLU 20 | R GLU 20 | 0.000 +/- 0.000 | -1.521 +/- 0.431 |
> > -0.527 +/- 1.684 | 0.859 +/- 1.585 | 0.000 +/- 0.000 | -1.189
> > +/- 0.539
> >
> > Then here is my question, Does the value after +/- sign stand for
> > standard deviation of the calculated energy, or standard error instead?
> >
> > Thanks & regards
> > Wei Liu
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
>
> ------------------------------
>
> Message: 10
> Date: Tue, 15 Sep 2015 08:48:45 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Regarding Simulations of Ionic Liquids on GPU
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20150915124845.GI75495.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Tue, Sep 15, 2015, MOHD HOMAIDUR RAHMAN wrote:
> >
> > I have a system that contains Ionic Liquids ( organic cation and
> inorganic
> > anion ) and we are simulating this systems by using Sander module with
> full
> > ewald (by EW_TYPE=1 keyword). The GPU version of simulation module PMEMD
> is
> > not supporting the full ewald method.
>
> There is generally no reason to use Ewald (as opposed to PME) for liquid
> state simulations. The sander program retains an Ewald option, but really
> only for the purpose of testing and validating PME parameters. PME is
> generally both much faster and more accurate than Ewald (unless you use a
> *very* large number of k-vectors in the Ewald sum).
>
> Amber has a tutorial on ionic liquids, and more information can be found
> here:
>
> %A K.G. Sprenger
> %A V.W. Jaeger
> %A J. Pfaendtner
> %T The General AMBER Force Field (GAFF) Can Accurately Predict
> Thermodynamic
> and Transport Properties of Many Ionic Liquids
> %J J. Phys. Chem. B
> %V 119
> %P 5882-5895
> %D 2015
>
> Note that it is not guaranteed that the GAFF force field will perform well
> without additional tweaking. (This statement is true for all GAFF
> applications, not just for ionic liquids.)
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 11
> Date: Tue, 15 Sep 2015 18:52:01 +0530
> From: ankita mehta <mehtaroadies.gmail.com>
> Subject: [AMBER] query
> To: amber.ambermd.org
> Message-ID:
> <
> CAMpjJqgtcu-MSCc6o7smmnec2BU3O6Kwgq0iUeMorwsbvyp-Lw.mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear All,
>
> I am trying to create topology and coordinate file for the pdb attached..
>
> It gives the warnings while reading the structure and when these warnings
> are ignored and toplogy and coordinate file is generated , structure is
> faulty ........
>
> Please tell how to overcome such warnings..how to generate successfully
> topology and coordinate files.
>
> Thanks!
>
> Ankita
>
> Fellow
>
> Imtech
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>
> ------------------------------
>
> Message: 12
> Date: Tue, 15 Sep 2015 09:38:05 -0400
> From: Kenneth Huang <kennethneltharion.gmail.com>
> Subject: [AMBER] query
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CALeh7kCiCuX0JL5JFOd2Ev+pHpBzXCAgDJTwWnzaACEvRHeLLw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Judging from your log, I'm guessing that residue 823 is a ligand or
> modified residue? What I think is going on is that the input you used had
> triplicate atom names, ie C1 is named C1 three times instead of C1, C1a,
> C1b, etc for whatever 823 is, hence the duplicate atom warning.
>
> Try renaming the atoms in 823 different names so that they don't appear
> more than once, and it should work.
>
> Best,
>
> Kenneth
>
> On Tuesday, September 15, 2015, ankita mehta <mehtaroadies.gmail.com>
> wrote:
>
> > Dear All,
> >
> > I am trying to create topology and coordinate file for the pdb attached..
> >
> > It gives the warnings while reading the structure and when these warnings
> > are ignored and toplogy and coordinate file is generated , structure is
> > faulty ........
> >
> > Please tell how to overcome such warnings..how to generate successfully
> > topology and coordinate files.
> >
> > Thanks!
> >
> > Ankita
> >
> > Fellow
> >
> > Imtech
> >
>
>
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
>
>
> ------------------------------
>
> Message: 13
> Date: Tue, 15 Sep 2015 17:11:40 +0300
> From: "Sofia Vasilakaki" <svasilak.chem.uoa.gr>
> Subject: [AMBER] sqm
> To: "AMBER Mailing List" <amber.ambermd.org>
> Message-ID:
> <c7fbfd1596f78817d97ed0492d562b4b.squirrel.webmail01.uoa.gr>
> Content-Type: text/plain;charset=utf-8
>
> Hi,
>
> Is it possible to use sqm for geometry optimization of a ligand and use
> the output for deriving AM1 or RESP charges in antechamber?
>
> Saying this, what is a typical input / output file for running sqm opt ?
> I think there is no tutorial about sqm and how to use it on its own.
>
> Thank you,
> Sofia V.
>
>
>
>
>
> ------------------------------
>
> Message: 14
> Date: Tue, 15 Sep 2015 15:18:09 +0100
> From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> Subject: Re: [AMBER] sqm
> To: <amber.ambermd.org>
> Message-ID: <20150915151809.026eec2d.zgb83773vig.dl.ac.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> On Tue, 15 Sep 2015 17:11:40 +0300
> Sofia Vasilakaki <svasilak.chem.uoa.gr> wrote:
>
> > Hi,
> >
> > Is it possible to use sqm for geometry optimization of a ligand and
> > use the output for deriving AM1 or RESP charges in antechamber?
>
> That's exactly what antechamber is doing for you. The charges are
> derived from the minimised structure. For RESP charges you would need
> to use other QM packages like GAMESS or Gaussian.
>
>
> Cheers,
> Hannes.
>
>
>
> ------------------------------
>
> Message: 15
> Date: Tue, 15 Sep 2015 10:27:42 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] mmpbsa error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3rU==
> 3dUAp5mVozLcjTz-obPFBYecD6Y0VqKUG0p9VnSw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Mon, Sep 14, 2015 at 9:40 PM, Lara rajam <lara.4884.gmail.com> wrote:
>
> > Dear Amber
> >
> > I am trying to do the MMPBSA calculation , earlier I was generating the
> > parameters with ff99SB and I was able to run mmpbsa.py
> >
> > Now I generated the prmtop using ff12SB , I was not able to run mmpbsa
> > calculation, the error is as below I am running in serial mode. I again
> > generated all the prmtop and did a try, the error is the same and my
> input
> > is below
> >
> > INPUT file
> >
> > Input file for running PB and GB in serial
> >
> > &general
> >
> > endframe=50, keep_files=2,
> >
> > /
> >
> > &gb
> >
> > igb=2, saltcon=0.100,
> >
> > /
> >
> > &pb
> >
> > istrng=0.100,
> >
> > /
> >
> >
> > OUT PUT ERROR !
> >
> > [TEST.NEMO dr2]$ $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o
> > FINAL_RESULTS_MMPBSA.dat -sp solvated_di.prmtop -cp complex.prmtop -rp
> > protein.prmtop -lp ligand.prmtop -y *.mdcrd
> >
> > Loading and checking parameter files for compatibility...
> >
> > mmpbsa_py_energy found! Using
> > /home/TEST/AMBERHOME/amber14/bin/mmpbsa_py_energy
> >
> > cpptraj found! Using /home/TEST/AMBERHOME/amber14/bin/cpptraj
> >
> > Preparing trajectories for simulation...
> >
> > 50 frames were processed by cpptraj for use in calculation.
> >
> >
> > Running calculations on normal system...
> >
> >
> > Beginning GB calculations with
> > /home/TEST/AMBERHOME/amber14/bin/mmpbsa_py_energy
> >
> > calculating complex contribution...
> >
> > File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA.py", line 96, in ?
> >
> > app.run_mmpbsa()
> >
> > File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA_mods/main.py", line 218,
> in
> > run_mmpbsa
> >
> > self.calc_list.run(rank, self.stdout)
> >
> > File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA_mods/calculation.py",
> line
> > 79, in run
> >
> > calc.run(rank, stdout=stdout, stderr=stderr)
> >
> > File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA_mods/calculation.py",
> line
> > 147, in run
> >
> > raise CalcError('%s failed with prmtop %s!' % (self.program,
> >
> > CalcError: /home/TEST/AMBERHOME/amber14/bin/mmpbsa_py_energy failed with
> > prmtop complex.prmtop!
> >
> ?
> This just says the energy calculation didn't work. It doesn't have the
> actual error message that says what went wrong.
>
> Look inside _MMPBSA_complex_gb.mdout.0 to see if the error message is
> there.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 16
> Date: Tue, 15 Sep 2015 17:29:45 +0300
> From: "Sofia Vasilakaki" <svasilak.chem.uoa.gr>
> Subject: Re: [AMBER] sqm
> To: "AMBER Mailing List" <amber.ambermd.org>
> Message-ID:
> <45b758f82021b7d72021ed65b87fda2d.squirrel.webmail01.uoa.gr>
> Content-Type: text/plain;charset=utf-8
>
> Ok. I thought you could use it separately using:
>
> sqm [-O] -i <input-file> -o <output-file>
>
> as it has been described in the manual.
>
> Thank you!
>
>
>
>
> > On Tue, 15 Sep 2015 17:11:40 +0300
> > Sofia Vasilakaki <svasilak.chem.uoa.gr> wrote:
> >
> >> Hi,
> >>
> >> Is it possible to use sqm for geometry optimization of a ligand and
> >> use the output for deriving AM1 or RESP charges in antechamber?
> >
> > That's exactly what antechamber is doing for you. The charges are
> > derived from the minimised structure. For RESP charges you would need
> > to use other QM packages like GAMESS or Gaussian.
> >
> >
> > Cheers,
> > Hannes.
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
>
> ------------------------------
>
> Message: 17
> Date: Tue, 15 Sep 2015 10:30:30 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] A question on binding free energy decomposition
> output
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3pOpt7rrWM5gvVWhvX8f9dnPUqu=
> CROcy7bNST2R9-UbA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Tue, Sep 15, 2015 at 2:22 AM, wliu <wliu.itcs.ecnu.edu.cn> wrote:
>
> > Dear all,
> >
> > I have a simple question about the output of binding free energy
> > decomposition. I calculated Per-residue energy decomposition for
> > specific residues with mmpbsa.py and I got the FINAL_DECOMP_MMPBSA.dat
> > file.
> >
> > DELTAS:
> > Total Energy Decomposition:
> > Residue | Location | Internal | van der Waals |
> > Electrostatic | Polar Solvation | Non-Polar Solv. |
> > TOTAL
> >
> >
> -------------------------------------------------------------------------------------------------------------------------------------------------------
> > LEU 18 | R LEU 18 | 0.000 +/- 0.000 | -2.968 +/- 0.505 |
> > -0.436 +/- 0.232 | 3.215 +/- 0.453 | 0.000 +/- 0.000 | -0.189
> > +/- 0.583
> > GLU 20 | R GLU 20 | 0.000 +/- 0.000 | -1.521 +/- 0.431 |
> > -0.527 +/- 1.684 | 0.859 +/- 1.585 | 0.000 +/- 0.000 | -1.189
> > +/- 0.539
> >
> > Then here is my question, Does the value after +/- sign stand for
> > standard deviation of the calculated energy, or standard error instead?
> >
>
> ?Standard deviation. It will also compute the standard error (via std.err
> = std.dev / sqrt(N) where N is the number of frames in the trajectory) and
> print that if you ask for CSV format decomposition output.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 18
> Date: Tue, 15 Sep 2015 10:33:10 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] sqm
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3rD7E6=
> te4c1UfkJ8B_zqFmqtiPE4CR0YMcy4ERnTQyVg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Tue, Sep 15, 2015 at 10:29 AM, Sofia Vasilakaki <svasilak.chem.uoa.gr>
> wrote:
>
> > Ok. I thought you could use it separately using:
> >
> > sqm [-O] -i <input-file> -o <output-file>
> >
> > as it has been described in the manual.
> >
>
> ?You can, but if your aim is to use SQM to minimize and derive AM1 charges,
> why not just use antechamber which does it all for you?
>
> And as far as I know, RESP requires Gaussian when using Amber (you can use
> GAMESS for R.E.D.).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 19
> Date: Tue, 15 Sep 2015 15:34:01 +0100
> From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> Subject: Re: [AMBER] sqm
> To: <amber.ambermd.org>
> Message-ID: <20150915153401.12d61c67.zgb83773vig.dl.ac.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> On Tue, 15 Sep 2015 17:29:45 +0300
> Sofia Vasilakaki <svasilak.chem.uoa.gr> wrote:
>
> > Ok. I thought you could use it separately using:
> >
> > sqm [-O] -i <input-file> -o <output-file>
> >
> > as it has been described in the manual.
>
>
> Of course, you can. Antechamber produces the input file (sqm.in) for
> you but running this would only give you the optimised structure and a
> set of Mulliken charges. You would then have to create an AC file from
> the sqm output and run it through am1bcc to obtain the charges.
> Alternatively, you can create input for the other QM packages.
> Antechamber can convert between quite a few input and output formats.
>
>
> Cheers,
> Hannes.
>
>
>
> ------------------------------
>
> Message: 20
> Date: Tue, 15 Sep 2015 11:52:33 -0400
> From: Xing <stecue.gmail.com>
> Subject: [AMBER] Has anyone tried VMD in the second step of tutorial
> A1?
> To: amber.ambermd.org
> Message-ID: <55F83EC1.4000600.gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear all,
>
> I'm trying to reproduce the step 2 of AMBER A1 tutorial with VMD (
> http://ambermd.org/tutorials/advanced/tutorial1/section2.htm) because
> Sirius is no longer available. However VMD can never
> superposition the "anchor atoms" and the two structures (linker and dye)
> cannot be aligned as shown in the tutorial. It seems that VMD cannot align
> a few atoms properly. My script is
>
> set anc_linker [atomselect 4 "index 5 4 6"]
> set anc_dye [atomselect 3 "index 7 6 4"]
> set linker_to_dye [measure fit $anc_linker $anc_dye]
> set all_linker [atomselect 4 "all"]
> $all_linker move $linker_to_dye
>
> It it adapted for protein alignment and works for many atoms... If there
> is nothing wrong in the script and VMD cannot do the alignment, what other
> software should I try?
>
> Thanks very much and best wishes,
> Xing
>
>
>
> ------------------------------
>
> Message: 21
> Date: Tue, 15 Sep 2015 18:06:34 +0200
> From: Ruth Helena Tichauer <rhtichau.laas.fr>
> Subject: [AMBER] vlimit exceeded and high temperature
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <9B1C6558-8A24-4AE1-9CA1-0D9472E4F3B0.laas.fr>
> Content-Type: text/plain; charset=utf-8
>
> Hi Amber community,
>
> I?m running a molecular dynamics simulation of a protein with its ligand
> and an Mg +2 ion in implicit solvent although there are tree water
> molecules in the active region as they are necessary for the reaction to
> proceed.
>
> The structure has been successfully quantum minimised (GMAX=40, RMS=1.8)
> prior to the MD; treating only a few residues, the ligand, the Mg ion and
> the water molecules quantum dynamically.
>
> I tried to run the molecular dynamics simulation treating quantum
> dynamically the same region of the system as during the minimisation but
> got an error message saying ?vlimit exceeded for step..?. Neither adding
> shake options, nor reducing the time step helped and, when the simulation
> was achieved, the temperature and the total energy were extremely high.
> Here is the input file:
>
> 100K temp QMMMMD
> &cntrl
> imin=0,
> ntb=0,
> igb=1,
> cut=12.0,
> tempi=0.0, temp0=100.0,
> ntc=2, ntf=2,
> ntt=3, gamma_ln=2.0,
> nstlim=1000, dt=0.0005,
> ntpr=1, ntwx=1,ifqnt=1,
> ntr=1,
> restraintmask = ':170,185,.CA,C,N',
> restraint_wt = 5.0
> /
> &qmmm
> qmmask=':59,61,168,169,186-188',
> qmcharge=-2,
> qm_theory='PM3',
> qmshake=0,
> qmcut=12.0,
> /
>
> I run then the same molecular dynamics simulation without the quantum
> treatment. It was successfully achieved but one of the water molecules had
> slipped away from the active site.. Only when restraining it with a force
> of 20 kcal/mol.A?2 it would remain in it.
>
> Here is the input file of the simulation when a water molecule "escapes":
>
> Heating 0 to 300K MD
> &cntrl
> imin=0,
> ntb=0,
> igb=1,
> cut=12.0,
> tempi=0.0, temp0=300.0,
> ntt=3, gamma_ln=2.0,
> nstlim=10000, dt=0.001,
> ntpr=100, ntwx=100,
> ntr=1,
> restraintmask = ':170,185,.CA,C,N',
> restraint_wt=10.0,
> /
>
> So I wander:
> _How a water molecule could go so far away?
> _Could the ?special routines? of shake used for water molecules be the
> reason of the ?vlimit exceeded? when they are treated quantum dynamically?
>
> Has anyone a clue of what I should add/change/remove?
>
> Thank you,
>
> Ruth
>
>
>
>
> ------------------------------
>
> Message: 22
> Date: Tue, 15 Sep 2015 12:50:37 -0400
> From: Lara rajam <lara.4884.gmail.com>
> Subject: Re: [AMBER] mmpbsa error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAPQ+66A_XNiT_x+1u8KnihWEPLxhiQS7o_pQMpFqZpzGh4_R=
> A.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Amber
>
> The error message was
>
> PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 2C
>
> I went through the earlier post and changed my input files as below
>
>
> input file for running PB and GB
>
> &general
>
> endframe=5000, keep_files=2,
>
> /
>
> &gb
>
> igb=2, saltcon=0.100,
>
> /
>
> &pb
>
> istrng=0.100,inp=1,radiopt=0,
>
> /
>
>
> The programing is working .
>
>
> I have a question if one need to calculate the binding energy (ligand ,
> Protein) is these inputs are enough if not what else to be added
>
>
> thank you
>
>
>
>
> On Tue, Sep 15, 2015 at 10:27 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > On Mon, Sep 14, 2015 at 9:40 PM, Lara rajam <lara.4884.gmail.com> wrote:
> >
> > > Dear Amber
> > >
> > > I am trying to do the MMPBSA calculation , earlier I was generating the
> > > parameters with ff99SB and I was able to run mmpbsa.py
> > >
> > > Now I generated the prmtop using ff12SB , I was not able to run mmpbsa
> > > calculation, the error is as below I am running in serial mode. I
> again
> > > generated all the prmtop and did a try, the error is the same and my
> > input
> > > is below
> > >
> > > INPUT file
> > >
> > > Input file for running PB and GB in serial
> > >
> > > &general
> > >
> > > endframe=50, keep_files=2,
> > >
> > > /
> > >
> > > &gb
> > >
> > > igb=2, saltcon=0.100,
> > >
> > > /
> > >
> > > &pb
> > >
> > > istrng=0.100,
> > >
> > > /
> > >
> > >
> > > OUT PUT ERROR !
> > >
> > > [TEST.NEMO dr2]$ $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o
> > > FINAL_RESULTS_MMPBSA.dat -sp solvated_di.prmtop -cp complex.prmtop -rp
> > > protein.prmtop -lp ligand.prmtop -y *.mdcrd
> > >
> > > Loading and checking parameter files for compatibility...
> > >
> > > mmpbsa_py_energy found! Using
> > > /home/TEST/AMBERHOME/amber14/bin/mmpbsa_py_energy
> > >
> > > cpptraj found! Using /home/TEST/AMBERHOME/amber14/bin/cpptraj
> > >
> > > Preparing trajectories for simulation...
> > >
> > > 50 frames were processed by cpptraj for use in calculation.
> > >
> > >
> > > Running calculations on normal system...
> > >
> > >
> > > Beginning GB calculations with
> > > /home/TEST/AMBERHOME/amber14/bin/mmpbsa_py_energy
> > >
> > > calculating complex contribution...
> > >
> > > File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA.py", line 96, in ?
> > >
> > > app.run_mmpbsa()
> > >
> > > File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA_mods/main.py", line
> 218,
> > in
> > > run_mmpbsa
> > >
> > > self.calc_list.run(rank, self.stdout)
> > >
> > > File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA_mods/calculation.py",
> > line
> > > 79, in run
> > >
> > > calc.run(rank, stdout=stdout, stderr=stderr)
> > >
> > > File "/home/TEST/AMBERHOME/amber14/bin/MMPBSA_mods/calculation.py",
> > line
> > > 147, in run
> > >
> > > raise CalcError('%s failed with prmtop %s!' % (self.program,
> > >
> > > CalcError: /home/TEST/AMBERHOME/amber14/bin/mmpbsa_py_energy failed
> with
> > > prmtop complex.prmtop!
> > >
> > ?
> > This just says the energy calculation didn't work. It doesn't have the
> > actual error message that says what went wrong.
> >
> > Look inside _MMPBSA_complex_gb.mdout.0 to see if the error message is
> > there.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 23
> Date: Tue, 15 Sep 2015 13:04:18 -0400
> From: Jonathan Gough <jonathan.d.gough.gmail.com>
> Subject: [AMBER] cyclic peptides and bond command in leap
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAFkCv1Sh3+hNSBdg7MwgC8vzBL9cMH83oS=
> BQn5rufjtsfZ34Q.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi All,
>
> I would like to simulate a (bi)cyclic peptide and I was wondering if anyone
> had any suggestions on how best to do parameterize/build this using
> (mostly) ff14SB via leap.
>
> I see from the List that one can simply make an alternate leaprc.ff14SB
> file that is absent of the terminal residues and then just draw a bond
> between the N and C terminus.
> http://archive.ambermd.org/201303/0171.html
>
> 1. Is this the best way to do it?
>
> 2. Can anyone provide an explanation of how "atoms" are defined in leap?
> Are they simply the variable given to the pdb dot residue# dot atom name
> (as per the manual trx.32.SG)? or are they the atom # from which they
> appear in the pdb file?
>
> 3. Within the peptide, I have an internal peptide(amide) bond LYS.NZ --
> ASP.CG. I understand i can use the bond command to create said bond, but
> is
> there a way to turn off the add missing atom function in leap? I can't seem
> to find a command to deleteAtom in leap.
>
> If I used gaff/antechamber to create a "new residue," I'm having a hard
> time wrapping my head around how to do it, would it be a single residue
> that appears 2x in the PDB? or would I just need to run the entire
> bi-cyclicpeptide through antechamber?
>
> I know I'm likely raising a lot of more complicated questions... but if I
> just wanted to get a basic idea of this thing in water.. I'm blocking on
> the best way to just generate a pseudo-reasonable set of parameters.
>
> Any help would be appreciated.
> Thanks,
> Jonathan
>
>
> ------------------------------
>
> Message: 24
> Date: Tue, 15 Sep 2015 13:25:48 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] mmpbsa error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3rBW8rK=
> Wy6r-Ofbfc+qGqRo5BHbpwLLURgpoNFujyKQg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Tue, Sep 15, 2015 at 12:50 PM, Lara rajam <lara.4884.gmail.com> wrote:
>
> > Dear Amber
> >
> > The error message was
> >
> > PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 2C
> >
> > I went through the earlier post and changed my input files as below
> >
> >
> > input file for running PB and GB
> >
> > &general
> >
> > endframe=5000, keep_files=2,
> >
> > /
> >
> > &gb
> >
> > igb=2, saltcon=0.100,
> >
> > /
> >
> > &pb
> >
> > istrng=0.100,inp=1,radiopt=0,
> >
> > /
> >
> >
> > The programing is working .
> >
> >
> > I have a question if one need to calculate the binding energy (ligand ,
> > Protein) is these inputs are enough if not what else to be added
> >
>
> ?Yes, these inputs will calculate a binding free energy using the PB and GB
> solvation models to estimate the solvation free energy contribution.
>
> It omits solute entropy contributions (e.g., from normal mode or
> quasi-harmonic approximations), but those are expensive and they do not
> always help. You should survey the literature for a more detailed
> discussion.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 25
> Date: Tue, 15 Sep 2015 14:31:34 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] query
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20150915183134.GB77720.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Tue, Sep 15, 2015, ankita mehta wrote:
>
> > I am trying to create topology and coordinate file for the pdb attached..
> >
> > It gives the warnings while reading the structure and when these warnings
> > are ignored and toplogy and coordinate file is generated , structure is
> > faulty ........
>
> To expand on the previous answer: read the warnings carefully. If you in
> fact
> have alternate conformers for residue 823 in your input pdb file, LEaP may
> be
> doing what you want (selecting the first conformer).
>
> >
> > Warning: Atom names in each residue should be unique.
> > (Same-name atoms are handled by using the first
> > occurrence and by ignoring the rest.
> > Frequently duplicate atom names stem from alternate
> > conformations in the PDB file.)
> >
>
> Since there weren't any other warnings (e.g. about missing heavy atoms),
> I'm
> guessing(?) that you have alternate conformers in the input PDB file.
>
> If that is correct, you will need to explain what you mean by the statement
> "structure is faulty".
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 26
> Date: Tue, 15 Sep 2015 14:39:57 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] sqm
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20150915183957.GC77720.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Tue, Sep 15, 2015, Sofia Vasilakaki wrote:
> >
> > Is it possible to use sqm for geometry optimization of a ligand and use
> > the output for deriving AM1 or RESP charges in antechamber?
>
> > Saying this, what is a typical input / output file for running sqm opt ?
>
> If you want to use sqm to geometry-optimize your molecule, set the "maxcyc"
> parameter (and maybe the "grms_tol" parameter) in the &qmmm namelist.
> See Section 9.3 of the Amber 2015 Reference Manual. There is an example
> input file in that section. Defaults for sqm will perform a geometry
> minimization with a reasonable (but not overly tight) convergence
> tolerance.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 27
> Date: Tue, 15 Sep 2015 18:38:43 +0000
> From: "Kalenkiewicz, Andrew (NIH/NICHD) [F]"
> <andrew.kalenkiewicz.nih.gov>
> Subject: [AMBER] Antechamber error
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID: <DDEBFE0D6BC5B94BB27C05168B7A2DC06EF157.msgb08.nih.gov>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Amber Mailing list,
>
> I am attempting to use a gaussian output file to generate a mol2 file with
> the correct information to generation force field libraries for an MD
> simulation. I tried the following command:
>
> antechamber -fi gout -fo mol2 -i gaussian.log -o mol.mol2 -c resp
>
> This invariably gives the error:
>
> Error: cannot run "/usr/local/apps/amber/amber14//bin/espgen -o
> ANTECHAMBER.ESP -i gaussian.log" in resp() of charge.c properly, exit
>
> The antechamber troubleshooting page<
> http://ambermd.org/antechamber/tips.html> seems to suggest that a
> possible source of error is that the coordinate information from the
> gaussian output file may have two many digits. However the correct solution
> to this problem is not entirely clear. I see this error message has shown
> up before in the Amber archives e.g. here:
> http://archive.ambermd.org/200910/0428.html
>
> Best wishes,
> Andrew
>
>
> ------------------------------
>
> Message: 28
> Date: Tue, 15 Sep 2015 14:52:01 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] vlimit exceeded and high temperature
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20150915185201.GE77720.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=utf-8
>
> On Tue, Sep 15, 2015, Ruth Helena Tichauer wrote:
> >
> > I?m running a molecular dynamics simulation of a protein with its
> > ligand and an Mg +2 ion in implicit solvent although there are tree
> > water molecules in the active region as they are necessary for the
> > reaction to proceed.
>
> I don't understand what you mean by the phrase "tree water molecule". (I
> first thought you meant to write "three", but this same phrase seems to
> persist in many emails....)
>
> >
> > The structure has been successfully quantum minimised (GMAX=40, RMS=1.8)
> > prior to the MD; treating only a few residues, the ligand, the Mg ion
> > and the water molecules quantum dynamically.
>
> This is not all that low an rms gradient; you might try more minimization.
>
> >
> > I tried to run the molecular dynamics simulation treating quantum
> > dynamically the same region of the system as during the minimisation but
> > got an error message saying ?vlimit exceeded for step..?.
>
> I don't see anything obviously wrong with your input file, so details are
> probably critical here.
>
>
> >
> > I run then the same molecular dynamics simulation without the quantum
> > treatment. It was successfully achieved but one of the water molecules
> > had slipped away from the active site..
> > _How a water molecule could go so far away?
>
> We don't have enough information here: do you see anything that should
> prevent
> the water molecule from diffusing away from the rest of the cluster?
>
> > _Could the ?special routines? of shake used for water molecules be
> > the reason of the ?vlimit exceeded? when they are treated quantum
> > dynamically?
>
> This seems unlikely. Since you saved a trajectory file from the qm/mm
> calculation at every step, look at it closely in a program like VMD or
> Chimera
> to see if you can figure out what bad things are happening. Compare it to
> a
> similar trajectory without qm/mm.
>
> ...good luck...dac
>
>
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 1343, Issue 1
> **************************************
>
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Received on Tue Sep 15 2015 - 21:30:03 PDT
