I am not recieving the amber problems and solution containing mails
On 5/24/12, amber-request.ambermd.org <amber-request.ambermd.org> wrote:
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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: problem installing AMBER12 on MacOSX (Philip Winter)
> 2. Re: The QMMM_MD err calculation of amber12+ gamessUS
> (Andreas Goetz)
> 3. Antechamber Atom Types (Sarah Edwards)
> 4. Re: mbondi3 (Jesper S?rensen)
> 5. Re: mbondi3 (Jason Swails)
> 6. Re: Antechamber Atom Types (David A. Case)
> 7. Re: mbondi3 (David A. Case)
> 8. problem with mol2 to pdb conversion (Chris Chris)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 23 May 2012 14:05:27 -0600
> From: Philip Winter <pwinter.ualberta.ca>
> Subject: Re: [AMBER] problem installing AMBER12 on MacOSX
> To: amber.ambermd.org
> Message-ID:
> <CA+z7t8QD8Hi=mrZXtm+xkpJdazx3YCV811WFgz=cukwbLUay7A.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Was any solution to this error found? We get the same error that Robert
> Oswald reported when compiling bintraj.F90 during the Amber 12 build
> process.
>
> Here was the system: New Mac Pro with Mac OS X 10.7.4 installed. Xcode
> 4.3.2 was installed. We tried compiling with the gcc/gfortran compilers
> from both the MacPorts packages gcc44 and also gcc46. All patches up to
> bugfix 7 for AmberTools and for Amber were applied.
>
> Compilation of Amber was successful with the -nobintraj configure option;
> but unfortunately we need the bintraj support.
>
> Strangely, I was able to compile successfully (no errors) on a MacBook Pro
> (2010 model) with the same versions of Mac OS, Xcode, and the MacPorts
> compiler packages listed above.
>
> Regards,
> Philip
>
> --
> Philip Winter
> Research Assistant, Experimental Oncology, University of Alberta
> Email: pwinter.ualberta.ca, Philip.Winter.albertahealthservices.ca
> Phone: (office) 780-643-4436, (cell) 780-233-7568
>
> From: Jason Swails
> <jason.swails.gmail.com<jason.swails.gmail.com?Subject=Re%3A%20%5BAMBER%5D%20problem%20installing%20AMBER12%20on%20MacOSX>>
>>
>> Date: Mon, 14 May 2012 08:38:25 -0700
>>
>> Just to check, then, what does
>>
>> gcc --version
>> gfortran --version
>>
>> return?
>>
>> On Mon, May 14, 2012 at 8:23 AM, Robert Oswald
>> <robert.oswald.gmail.com>wrote:
>>
>>
>> *> Jason, *
>> *> As far as I know I am using the exact compilers in the example on the
>> wiki: *
>> *> *
>> *> port select --list gcc *
>> *> Available versions for gcc: *
>> *> gcc42 *
>> *> llvm-gcc42 *
>> *> mp-gcc44 (active) *
>> *> none *
>> *> *
>> *> I have applied the bugfix to AmberTools as you suggested. *
>> *> Robert *
>> *> *
>> *> On Mon, May 14, 2012 at 11:11 AM, Jason Swails <jason.swails.gmail.com
>> *
>> *> >wrote: *
>> *> *
>> *> > What version of the GNU compilers are you using? *
>> *> > *
>> *> > My suggestion is to use the exact compilers used in the example on
>> the *
>> *> wiki *
>> *> > you were following. *
>> *> > *
>> *> > Also, the real8 problem should have been fixed by a bugfix to
>> AmberTools. *
>> *> > Please check that you have all bugfixes applied. (Since you applied
>> one *
>> *> by *
>> *> > hand, use the command: *
>> *> > *
>> *> > ./patch_amber.py --update --ignore-fails *
>> *> > ) *
>> *> > *
>> *> > HTH, *
>> *> > Jason *
>> *> > *
>> *> > On Mon, May 14, 2012 at 8:06 AM, Robert Oswald <
>> robert.oswald.gmail.com *
>> *> > >wrote: *
>> *> > *
>> *> > > I am trying to install AmberTools12 and Amber12 on Mac OS X
>> (10.7.3) *
>> *> > > following exactly the procedure described in: *
>> *> > > *
>> *> > > http://jswails.wikidot.com/installing-amber12-and-ambertools-12 *
>> *> > > *
>> *> > > I had no problem installing AmberTools12 alone (except for having
>> to *
>> *> fix *
>> *> > > the real8 problem in psfprm.F90). Installing with Amber 12, I have
>> run *
>> *> > into *
>> *> > > the following issue: *
>> *> > > *
>> *> > > gfortran -DBINTRAJ -c -O3 -mtune=native -ffree-form *
>> *> > > -I../../AmberTools/src/pbsa -I../../AmberTools/src/sqm *
>> *> > > -I../../AmberTools/src/rism -I../../include *
>> *> > > -I/Users/reo1/Documents/amber12/include *
>> *> > > -I/Users/reo1/Documents/amber12/include -o bintraj.o bintraj.F90 *
>> *> > > bintraj.F90:119.27: *
>> *> > > *
>> *> > > call checkNCerror(nf90_put_att(vel_ncid, VelocVarID, *
>> *> > > "scale_factor", & *
>> *> > > 1 *
>> *> > > Error: Generic function 'nf90_put_att' at (1) is not consistent
>> with a *
>> *> > > specific intrinsic interface *
>> *> > > make[2]: *** [bintraj.o] Error 1 *
>> *> > > make[1]: *** [serial] Error 2 *
>> *> > > make: *** [install] Error 2 *
>> *> > > *
>> *> > > I'd be grateful for any help in resolving this problem. *
>> *> > > Thanks, *
>> *> > > Robert Oswald *
>> *> > > *
>> *> > > *
>> *> > > -- *
>> *> > > ******************************************** *
>> *> > > Robert Oswald *
>> *> > > Department of Molecular Medicine *
>> *> > > Cornell University *
>> *> > > Ithaca, NY 14850 *
>> *> > > _______________________________________________ *
>> *> > > AMBER mailing list *
>> *> > > AMBER.ambermd.org *
>> *> > > http://lists.ambermd.org/mailman/listinfo/amber *
>> *> > > *
>> *> > *
>> *> > *
>> *> > *
>> *> > -- *
>> *> > Jason M. Swails *
>> *> > Quantum Theory Project, *
>> *> > University of Florida *
>> *> > Ph.D. Candidate *
>> *> > 352-392-4032 *
>> *> > _______________________________________________ *
>> *> > AMBER mailing list *
>> *> > AMBER.ambermd.org *
>> *> > http://lists.ambermd.org/mailman/listinfo/amber *
>> *> > *
>> *> *
>> *> *
>> *> *
>> *> -- *
>> *> ******************************************** *
>> *> Robert Oswald *
>> *> Department of Molecular Medicine *
>> *> Cornell University *
>> *> Ithaca, NY 14850 *
>> *> _______________________________________________ *
>> *> AMBER mailing list *
>> *> AMBER.ambermd.org *
>> *> http://lists.ambermd.org/mailman/listinfo/amber *
>> *> *
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing
>> listAMBER.ambermd.orghttp://lists.ambermd.org/mailman/listinfo/amber
>>
>> Received on Mon May 14 2012 - 09:00:04 PDT
>>
>>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 23 May 2012 13:22:53 -0700
> From: Andreas Goetz <agoetz.sdsc.edu>
> Subject: Re: [AMBER] The QMMM_MD err calculation of amber12+ gamessUS
> To: javacfish <javacfish.yahoo.com.cn>, AMBER Mailing List
> <amber.ambermd.org>
> Message-ID: <DB685341-AE5C-412C-ACE6-9D9497427751.sdsc.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Please read the manual and the error message in the output: The AMBER
> interface to GAMESS does not support QM/MM (unless you use mechanical
> embedding). You have to use one of the supported QM packages.
>
> All the best,
> Andy
>
> On May 18, 2012, at 2:52 AM, javacfish wrote:
>
>> Hello all,
>>
>> I modify the tutorial of amber website
>> http://ambermd.org/tutorials/advanced/tutorial2/section3.htm , I set
>> qmmask=':1-2' for QM region, the other is set as MM region. The detail
>> parameters is set as below:
>>
>> ###################################################################################
>> &cntrl
>> imin=1, ! do a minimization
>> maxcyc=500, ! max 2 minimization steps
>> ncyc=200, ! switch to conjugate gradient after 2 steps of steepest
>> descent
>> drms=0.5, ! RMS gradient convergence criterium 0.5 (kcal/mol)/A =
>> 2.d-3 au
>> cut=8.0, ! non-bonded cutoff (irrelevant for now with pure QM)
>> ntb=1, ! no periodic boundary conditions
>> ntpr=1, ! print every minimization step
>> ntwx=1, ! write coordinates each step
>> ntwr=2, ! write restart file each 10 steps
>> ioutfm = 1, ! NetCDF MDCRD.
>> ifqnt=1 ! do QM/MM
>> /
>> &qmmm
>> qmmask =':1-2',
>> qmcharge = 0,
>> qm_ewald = 0,
>> qm_theory ='EXTERN',
>> qmcut = 8.0,
>> adjust_q = 0,
>> verbosity = 0,
>> /
>> &gms
>> gms_version = '00',
>> num_threads = $GMS_NCPUS,
>> basis = '6-31G',
>> scf_conv = 1.0D-05,
>> charge = 0,
>> chelpg = 1,
>> mwords = 50,
>> dipole = 1,
>> /
>> ############################################################################################
>>
>>
>> But when I run the QMMM_MD calculation, the err happens as below:
>>
>>
>> *********************************************************************
>> --------------------------------------------------------------------------------
>> 3.1 QM CALCULATION INFO
>> --------------------------------------------------------------------------------
>> SANDER BOMB in subroutine qm2_extern_get_qm_forces
>> nquant /= natom
>> gms does not support QM/MM
>> *********************************************************************
>>
>>
>> So what is the wrong with the calculation of amber+gamessUS? Who can help
>> me?
>>
>> Thanks!
>>
>> javacfish
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel : +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web : www.awgoetz.de
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 23 May 2012 16:43:07 -0500
> From: Sarah Edwards <sarah.sarahjedwards.com>
> Subject: [AMBER] Antechamber Atom Types
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CADXS=KANo-ZbZfBzyHgBDfEaAfobpCNDEi9D_oJVvxyeejxY=A.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I am currently trying to create a Boron atom type using antechamber and
> have run into an issue: antechamber does not recognize Boron.
>
> The instructions I have been following to create a frcmod file from CB.pdb
> are two steps as follows:
>
> antechamber -i CB.pdb -fi pdb -o CB.prepin -fo prepi -c bcc -j 4 -at gaff
>
> parmchk -i CB.prepin -o CB.frcmod -f prepi
>
> The "antechamber" stage gives an output with blank spaces for the Boron
> atoms. Is there a way to tell antechamber about new atoms?
>
> Thanks!
>
> Sarah
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 23 May 2012 15:21:21 -0700
> From: Jesper S?rensen <jesorensen.ucsd.edu>
> Subject: Re: [AMBER] mbondi3
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <AA2147D7-4457-4B5B-B388-1C5DF3C573B8.ucsd.edu>
> Content-Type: text/plain; charset=iso-8859-1
>
> Hi Jason,
>
> Thanks for pointing me in the right direction. I have one follow up
> question. In the code snippet here below the C1, C2, and C3 atomtypes, am I
> correct if I think these are either united-atoms (e.g. CH3) or belonging to
> NA (e.g. C1')?
>
> if molecule.elements[i] == 'C':
> if parm.parm_data['AMBER_ATOM_TYPE'][i][:2] in ['C1', 'C2', 'C3']:
> parm.parm_data['RADII'][i] = 2.2
> else:
> parm.parm_data['RADII'][i] = 1.7
>
> Best,
> Jesper
>
>
>
>
> On May 20, 2012, at 3:59 PM, Jason Swails wrote:
>
>> In parmed you can look in Ambertools/src/parmed/ParmedTools/changeradii.py
>> (i think, i dont have the source handy to confirm) for the rules.
>> Hopefully it is easy enough to glean from the source code there (it is
>> trickier in the leap sources, IMO).
>>
>> HTH,
>> Jason
>>
>> --
>> Jason Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>>
>> On May 17, 2012, at 8:26 AM, Jesper S?rensen <jesorensen.ucsd.edu> wrote:
>>
>>> Hi Jason,
>>>
>>> This is an old posting, but could you point me to the place where these
>>> atom radii are stored in the source code, either for Leap or ParmEd?
>>>
>>> I want to try and make a radii/charges file for pdb2pqr, to generate e.g.
>>> bondi radii and amber charges, to be used for PB calculations with APBS
>>> or DELPHI.
>>>
>>> Thanks,
>>> Jesper
>>>
>>>
>>>
>>> On May 2, 2012, at 1:07 PM, Jason Swails wrote:
>>>
>>>> What Hai was saying is that "set default pbradii mbondi3" is identical
>>>> to
>>>> "set default pbradii mbondi2" for all atoms except 3 atom types
>>>> [HH(Arg)
>>>> and OE(Glu), OD(Asp)].
>>>>
>>>> Also, the atom radii are NOT stored in the force field files (e.g.,
>>>> gaff.dat, parm99.dat, etc.). They are stored in the LEaP (and ParmEd)
>>>> source code. If you want to use the mbondi3 radii, you should load
>>>> mbondi3
>>>> at the beginning -- the ligand will be treated as though the radii set
>>>> was
>>>> mbondi2.
>>>>
>>>> HTH,
>>>> Jason
>>>>
>>>> On Wed, May 2, 2012 at 11:05 AM, Jesper S?rensen
>>>> <jesorensen.ucsd.edu>wrote:
>>>>
>>>>> Thank you Hai. But it is likely that the ligand radii are coming from
>>>>> the
>>>>> GAFF parameters.
>>>>>
>>>>> I wonder if the correct procedure would probably be to "set default
>>>>> PBradii mbondi3" before loading in the ligand - then only the protein
>>>>> radii
>>>>> should change to mbondi3, without trying to alter the ligand radii as
>>>>> well,
>>>>> which again mbondi3 was likely not parameterized for?
>>>>>
>>>>> Or will this also change the ligand radii?
>>>>>
>>>>> Best,
>>>>> Jesper
>>>>>
>>>>>
>>>>>>
>>>>>> For the ligand, mbondi3 should be exactly the same as mbondi2 since
>>>>>> only
>>>>>> radii of HH(Arg) and OE(Glu), OD(Asp) atom type are changed in
>>>>>> mbondi3
>>>>> from
>>>>>> mbondi2.
>>>>>>
>>>>>> Best
>>>>>> NHAI
>>>>>>
>>>>>>
>>>>>> On Apr 30, 2012, at 9:02 AM, Ray Luo, Ph.D. wrote:
>>>>>>
>>>>>>> Jesper,
>>>>>>>
>>>>>>> Just a comment on a specific point in your email ...
>>>>>>>
>>>>>>> If you set radiopt=1 and have ligand (GAFF atoms) in the system,
>>>>>>> PBSA
>>>>>>> would drop a bomb and quit. I believe this is the designed behavior.
>>>>>>> This is because we don't have a "rule" to define the generic atomic
>>>>>>> types in organic molecules. As you can image, the rule would require
>>>>>>> far more simulation data to summarize than that for the
>>>>>>> proteins/NAs.
>>>>>>>
>>>>>>> So I don't think the scenario in your email would occur.
>>>>>>>
>>>>>>> If you have ligand (GAFFs), the only radii you can use with PBSA
>>>>>>> right
>>>>>>> now is those in the prmtop file and those can be read in by "radiopt
>>>>>>> =
>>>>>>> 0".
>>>>>>>
>>>>>>> It's not easy to mix different radii set for proteins/NAs and ligand
>>>>>>> unless you can somehow revise the radii section in the prmtop file.
>>>>>>>
>>>>>>> Ray
>>>>>>>
>>>>>>> On Mon, Apr 30, 2012 at 12:11 AM, Jesper S?rensen
>>>>>>> <jesorensen.ucsd.edu>
>>>>> wrote:
>>>>>>> ...
>>>>>>>> I know (Ambertools 12, section 8.2.3) that PBSA if you use
>>>>> (radiopt=1), will stick to the Antechamber/GAFF radii for the ligand
>>>>> (and
>>>>> perhaps even the FF radii for the protein) if there are GAFF
>>>>> parameters
>>>>> present in the prmtop file, instead of swithing to the Tan & Luo radii
>>>>> (TYL06 radii). But perhaps this is only a requirement for the TYL06
>>>>> radii
>>>>> and not mbondi* radii? Can you clarify this a bit for me?
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> Jesper
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Jason M. Swails
>>>> Quantum Theory Project,
>>>> University of Florida
>>>> Ph.D. Candidate
>>>> 352-392-4032
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 24 May 2012 10:25:42 +1000
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] mbondi3
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <9AEC9CCF-8222-4526-9BA5-E75A001C184A.gmail.com>
> Content-Type: text/plain; charset=utf-8
>
>
>
> On May 24, 2012, at 8:21 AM, Jesper S?rensen <jesorensen.ucsd.edu> wrote:
>
>> Hi Jason,
>>
>> Thanks for pointing me in the right direction. I have one follow up
>> question. In the code snippet here below the C1, C2, and C3 atomtypes, am
>> I correct if I think these are either united-atoms (e.g. CH3) or belonging
>> to NA (e.g. C1')?
>
> I'm not sure. Keep in mind this is atom type, not atom name. Therefore the
> nucleic acid reasoning is probably not justified (although still possible).
>
>
> The atom types may be described via a comment in the parm*.dat files. You
> can also look at what atoms have these types in the standard library files
> (see http://ambermd.org/formats.html for a description of the OFF library
> format do you can see which are the atom types).
>
> The leap files are in AMBERHOME/dat/leap
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 23 May 2012 21:42:59 -0400
> From: "David A. Case" <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] Antechamber Atom Types
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20120524014259.GA3589.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Wed, May 23, 2012, Sarah Edwards wrote:
>
>> I am currently trying to create a Boron atom type using antechamber and
>> have run into an issue: antechamber does not recognize Boron.
>
> There is no simple fix for this. Boron chemistry is quite unique, and
> there
> is no support for it.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 23 May 2012 21:44:28 -0400
> From: "David A. Case" <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] mbondi3
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20120524014428.GB3589.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=iso-8859-1
>
> On Wed, May 23, 2012, Jesper S?rensen wrote:
>>
>> In the code snippet here below the C1, C2, and C3 atomtypes,
>> am I correct if I think these are either united-atoms (e.g. CH3) or
>> belonging to NA (e.g. C1')?
>
> The former, which is why you get such big radii for C1, C2, C3.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Mon, 21 May 2012 20:46:04 -0700 (PDT)
> From: Chris Chris <alpharecept.yahoo.com>
> Subject: [AMBER] problem with mol2 to pdb conversion
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <1337658364.65644.YahooMailNeo.web111803.mail.gq1.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
> I am trying to convert a mol2 file into a pdb (using Vega ZZ.). I start with
> test.mol2- which has both the ligand and and the protein- but when I save as
> a pdb in Vega ZZ (test_vega.pdb), only the protein is written in the pdb and
> the ligand is not included. I notice that the connect info in the mol2
> (test.mol2) comes before the ligand coordinates- does the connect
> information cause the reading to stop? I want to put this complex into
> antechamber but I have been having problems generating the pdb file for the
> complex.
>
> Thanks for any help
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> ------------------------------
>
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>
>
> End of AMBER Digest, Vol 162, Issue 3
> *************************************
>
--
jit mukherjee
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Received on Wed May 23 2012 - 22:00:02 PDT
