- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>

Date: Fri, 13 Jun 2014 13:42:31 +0200

As per current AMBER QM/MM goes I think it supports following

Support is provided for the PM3, PDDG/PM3, PM3CARB1, AM1, MNDO, and

PDDG/MNDO semi-empirical Hamiltonians as well as the self-consistent charge

density functional tight binding (SCC-DFTB) method.

Check this http://www.ncbi.nlm.nih.gov/pubmed/18072177

On Fri, Jun 13, 2014 at 1:36 PM, Soumendranath Bhakat <

bhakatsoumendranath.gmail.com> wrote:

*> Use DFTB keyword in the qmtheory part. Check back the tutorial here
*

*> http://ambermd.org/tutorials/advanced/tutorial2/section3.htm
*

*>
*

*>
*

*> On Fri, Jun 13, 2014 at 1:34 PM, Soumendranath Bhakat <
*

*> bhakatsoumendranath.gmail.com> wrote:
*

*>
*

*>> As per as my understanding goes you should make sure which residues or
*

*>> atoms you want to traet will which level of QM parameter that you can
*

*>> easily do using qmmask. Flag ifqnt will tell Amber that you want a QM/MM
*

*>> run. You can download the files to check the optimized structure.Quick look
*

*>> bu downloading the trajectory and focus on QM/MM region you treated.
*

*>>
*

*>>
*

*>> On Fri, Jun 13, 2014 at 1:26 PM, Kshatresh Dutta Dubey <
*

*>> kshatresh.gmail.com> wrote:
*

*>>
*

*>>> Dear Jason,
*

*>>>
*

*>>> I am looking for QM optimization, I know that using imin=1 will give
*

*>>> me
*

*>>> minimized structure but I think that it will molecular mechanically
*

*>>> minimize the system, but what for QM optimizations? If I have to use
*

*>>> sander for minimization then what is the use of implementation of
*

*>>> Gaussian
*

*>>> interface? I am curious to know that - is it possible to perform QM
*

*>>> optimization of QM region using external QM program and sander for MM
*

*>>> region. If yes then what should I do? Using following input (complete
*

*>>> input, I used) does not optimize the QM region, it does single point
*

*>>> energy
*

*>>> calculations only, while sander does optimize MM region.
*

*>>>
*

*>>> *QM-MM calculations for FMN domain *
*

*>>> *&cntrl*
*

*>>> * imin=1, maxcyc=10,*
*

*>>> * ntb=0,*
*

*>>> * cut=20.,*
*

*>>> * ifqnt=1*
*

*>>> * /*
*

*>>> * &qmmm*
*

*>>> * qmmask ='.819-830,2244-2295',*
*

*>>> * qmcharge=0,*
*

*>>> * spin =1,*
*

*>>> * qm_theory='EXTERN',*
*

*>>> * qmcut=20.0*
*

*>>> * /*
*

*>>> * &gau*
*

*>>> * mem = '2GB'*
*

*>>> *! method = 'B3LYP',*
*

*>>> *! basis = '6-31G',*
*

*>>> * use_template =1,*
*

*>>> * num_threads = 2*
*

*>>> * /*
*

*>>>
*

*>>> Thanks and regards
*

*>>> Kshatresh
*

*>>>
*

*>>>
*

*>>>
*

*>>> On Fri, Jun 13, 2014 at 2:01 PM, Soumendranath Bhakat <
*

*>>> bhakatsoumendranath.gmail.com> wrote:
*

*>>>
*

*>>> > Use these input for minimization if you are using QM/MM. Please use
*

*>>> sander
*

*>>> > and sander.MPI for running
*

*>>> >
*

*>>> > Full_Mini.in
*

*>>> >
*

*>>> > Initial minimization of QMMM: solvent molecules and added ions
*

*>>> > &cntrl
*

*>>> > imin = 1,
*

*>>> > maxcyc = 2500,
*

*>>> > ncyc = 750,
*

*>>> > ntb = 1,
*

*>>> > ntr = 1,
*

*>>> > cut = 12.0,
*

*>>> > ifqnt = 1,
*

*>>> > /
*

*>>> > &qmmm
*

*>>> > qmmask= '557,250,238.75,86,89,75',
*

*>>> > qmcharge=0,
*

*>>> > qmtheory=7, *(please suggest check once)*
*

*>>> > qmshake=1,
*

*>>> > qm_ewald=1,
*

*>>> > qm_pme=1,
*

*>>> > /
*

*>>> >
*

*>>> > Hold the Protein fixed
*

*>>> > 10.0
*

*>>> > RES 1 557
*

*>>> >
*

*>>> > All the best.
*

*>>> >
*

*>>> >
*

*>>> > On Fri, Jun 13, 2014 at 12:54 PM, Jason Swails <jason.swails.gmail.com
*

*>>> >
*

*>>> > wrote:
*

*>>> >
*

*>>> > >
*

*>>> > >
*

*>>> > > > On Jun 13, 2014, at 5:50 AM, Kshatresh Dutta Dubey <
*

*>>> > kshatresh.gmail.com>
*

*>>> > > wrote:
*

*>>> > > >
*

*>>> > > > Dear Prof Monard,
*

*>>> > > >
*

*>>> > > > Many thanks for your quick response, still I am unable to find
*

*>>> any
*

*>>> > > > keyword that handles the optimizing process in sander. I went
*

*>>> through
*

*>>> > the
*

*>>> > > > manual bt I was unable to find such keyword. I will deeply
*

*>>> appreciate
*

*>>> > you
*

*>>> > > > if you help me to handle this process so that I can get proper QM
*

*>>> > > > optimization.
*

*>>> > > > Thanking you again.
*

*>>> > >
*

*>>> > > What you're looking for is a basic minimization. Look at the imin and
*

*>>> > > ntmin flags.
*

*>>> > >
*

*>>> > > HTH,
*

*>>> > > Jason
*

*>>> > >
*

*>>> > > >
*

*>>> > > >
*

*>>> > > >
*

*>>> > > > On Fri, Jun 13, 2014 at 12:31 PM, Gerald Monard <
*

*>>> > > > Gerald.Monard.univ-lorraine.fr> wrote:
*

*>>> > > >
*

*>>> > > >> Hi,
*

*>>> > > >>
*

*>>> > > >> You cannot use the Gaussian optimizer since it is sander that
*

*>>> masters
*

*>>> > > >> what happens to the coordinates (from a coordinate set, sander
*

*>>> asks
*

*>>> > > >> gaussian to compute an energy, it does not let gaussian modify
*

*>>> them,
*

*>>> > > >> hence the "force" keyword).
*

*>>> > > >> You'd better use one of the optimizers available in sander (&cntrl
*

*>>> > > >> namelist) instead.
*

*>>> > > >>
*

*>>> > > >> Gerald.
*

*>>> > > >>
*

*>>> > > >>
*

*>>> > > >>> On 06/13/2014 11:16 AM, Kshatresh Dutta Dubey wrote:
*

*>>> > > >>> Dear Users
*

*>>> > > >>>
*

*>>> > > >>> I am using Amber 14 for QM/MM calculation with Gaussian as
*

*>>> > external
*

*>>> > > >>> interface. I have to optimize a system containing some amino
*

*>>> acids
*

*>>> > and
*

*>>> > > a
*

*>>> > > >>> ligand in QM regions. I found that Amber automatically adds some
*

*>>> > > keywords
*

*>>> > > >>> in route section of Gaussian input that force Gaussian to do
*

*>>> single
*

*>>> > > point
*

*>>> > > >>> calculations. For example, I used :
*

*>>> > > >>> *&gau*
*

*>>> > > >>> * mem = '2GB'*
*

*>>> > > >>> *! method = 'B3LYP',*
*

*>>> > > >>> *! basis = '6-31G',*
*

*>>> > > >>> * use_template =1,*
*

*>>> > > >>> * num_threads = 2*
*

*>>> > > >>> * /*
*

*>>> > > >>> for &gau namelist and :
*

*>>> > > >>>
*

*>>> > > >>> *#P OPT B3LYP/6-31G SCF=(Conver=8)*
*

*>>> > > >>>
*

*>>> > > >>> for template file namelist. The calculations runs fine and it
*

*>>> shows
*

*>>> > > >> normal
*

*>>> > > >>> termination, but I found that it does only single point
*

*>>> calculation
*

*>>> > not
*

*>>> > > >>> optimizing the structure while I have mentioned optimization in
*

*>>> route
*

*>>> > > >>> sections. I notice that Amber adds some additional keyword such
*

*>>> as
*

*>>> > > >> 'Force'
*

*>>> > > >>> in route section which restricts Gaussian to calculate forces
*

*>>> only. I
*

*>>> > > >> guess
*

*>>> > > >>> it is fine for QM-MM/MD since we need forces for dynamics, but
*

*>>> here I
*

*>>> > > am
*

*>>> > > >>> interested in QM/MM optimization only. The route section
*

*>>> modified by
*

*>>> > > >> Amber
*

*>>> > > >>> is :
*

*>>> > > >>>
*

*>>> > > >>> *#P OPT B3LYP/6-31G SCF=(Conver=8) NoSymm Force Guess=Read Charge
*

*>>> > > Prop=*
*

*>>> > > >>> * (Field,Read)*
*

*>>> > > >>>
*

*>>> > > >>> How can I disable 'Force' keyword so that I can perform proper
*

*>>> > > >>> optimization. I will be thankful for your help.
*

*>>> > > >>>
*

*>>> > > >>> thanks
*

*>>> > > >>
*

*>>> > > >> --
*

*>>> > > >>
*

*>>> > > >>
*

*>>> > >
*

*>>> >
*

*>>> ____________________________________________________________________________
*

*>>> > > >>
*

*>>> > > >> Prof. Gerald MONARD
*

*>>> > > >> SRSMC, Université de Lorraine, CNRS
*

*>>> > > >> Boulevard des Aiguillettes B.P. 70239
*

*>>> > > >> F-54506 Vandoeuvre-les-Nancy, FRANCE
*

*>>> > > >>
*

*>>> > > >> e-mail : Gerald.Monard.univ-lorraine.fr
*

*>>> > > >> tel. : +33 (0)383.684.381
*

*>>> > > >> fax : +33 (0)383.684.371
*

*>>> > > >> web : http://www.monard.info
*

*>>> > > >>
*

*>>> > > >>
*

*>>> > > >>
*

*>>> > >
*

*>>> >
*

*>>> ____________________________________________________________________________
*

*>>> > > >>
*

*>>> > > >>
*

*>>> > > >> _______________________________________________
*

*>>> > > >> AMBER mailing list
*

*>>> > > >> AMBER.ambermd.org
*

*>>> > > >> http://lists.ambermd.org/mailman/listinfo/amber
*

*>>> > > >
*

*>>> > > >
*

*>>> > > >
*

*>>> > > > --
*

*>>> > > > With best regards
*

*>>> > > >
*

*>>> > >
*

*>>> >
*

*>>> ************************************************************************************************
*

*>>> > > > Dr. Kshatresh Dutta Dubey
*

*>>> > > > Post Doctoral Researcher,
*

*>>> > > > c/o Prof Sason Shaik,
*

*>>> > > > Hebrew University of Jerusalem, Israel
*

*>>> > > > Jerusalem, Israel
*

*>>> > > > _______________________________________________
*

*>>> > > > AMBER mailing list
*

*>>> > > > AMBER.ambermd.org
*

*>>> > > > http://lists.ambermd.org/mailman/listinfo/amber
*

*>>> > >
*

*>>> > > --
*

*>>> > > Jason M. Swails
*

*>>> > > BioMaPS,
*

*>>> > > Rutgers University
*

*>>> > > Postdoctoral Researcher
*

*>>> > > _______________________________________________
*

*>>> > > AMBER mailing list
*

*>>> > > AMBER.ambermd.org
*

*>>> > > http://lists.ambermd.org/mailman/listinfo/amber
*

*>>> > >
*

*>>> >
*

*>>> >
*

*>>> >
*

*>>> > --
*

*>>> > Thanks & Regards;
*

*>>> > Soumendranath Bhakat
*

*>>> > _______________________________________________
*

*>>> > AMBER mailing list
*

*>>> > AMBER.ambermd.org
*

*>>> > http://lists.ambermd.org/mailman/listinfo/amber
*

*>>> >
*

*>>>
*

*>>>
*

*>>>
*

*>>> --
*

*>>> With best regards
*

*>>>
*

*>>> ************************************************************************************************
*

*>>> Dr. Kshatresh Dutta Dubey
*

*>>> Post Doctoral Researcher,
*

*>>> c/o Prof Sason Shaik,
*

*>>> Hebrew University of Jerusalem, Israel
*

*>>> Jerusalem, Israel
*

*>>> _______________________________________________
*

*>>> AMBER mailing list
*

*>>> AMBER.ambermd.org
*

*>>> http://lists.ambermd.org/mailman/listinfo/amber
*

*>>>
*

*>>
*

*>>
*

*>>
*

*>> --
*

*>> Thanks & Regards;
*

*>> Soumendranath Bhakat
*

*>>
*

*>>
*

*>
*

*>
*

*> --
*

*> Thanks & Regards;
*

*> Soumendranath Bhakat
*

*>
*

*>
*

Date: Fri, 13 Jun 2014 13:42:31 +0200

As per current AMBER QM/MM goes I think it supports following

Support is provided for the PM3, PDDG/PM3, PM3CARB1, AM1, MNDO, and

PDDG/MNDO semi-empirical Hamiltonians as well as the self-consistent charge

density functional tight binding (SCC-DFTB) method.

Check this http://www.ncbi.nlm.nih.gov/pubmed/18072177

On Fri, Jun 13, 2014 at 1:36 PM, Soumendranath Bhakat <

bhakatsoumendranath.gmail.com> wrote:

-- Thanks & Regards; Soumendranath Bhakat _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Jun 13 2014 - 06:00:04 PDT

Custom Search