Hi,
On Tue, Sep 15, 2015 at 10:11 PM, Sehrish Naz <mjazse.gmail.com> wrote:
> 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
Could you provide some more details about what is not correct about
the plots? Maybe attach them if they are not too big (or send them to
me directly).
I can say that if you want the 'sumout' file to have Grace format you
need to give it the '.agr' extension only, e.g.
secstruct : 1-336 out dssp.gnu sumout dssp.agr
Cpptraj tries to determine output file format based on file name
extension, and '.sum' will default to the standard column data format.
-Dan
> 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
>> -------------- next part --------------
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>> Desc: not available
>> Url :
>> http://lists.ambermd.org/mailman/private/amber/attachments/20150915/5c3358ac/attachment-0001.pdb
>> -------------- next part --------------
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>> Url :
>> http://lists.ambermd.org/mailman/private/amber/attachments/20150915/5c3358ac/attachment-0001.bin
>>
>> ------------------------------
>>
>> 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
>> **************************************
>>
> _______________________________________________
> 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)
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 16 2015 - 08:30:08 PDT
