Dear Sir
thank you, actually I want to simulate the tubulin protein with drug for
its interaction,
hence i want to use sander for GB simulation.
thanks in advance
On Mon, Aug 25, 2014 at 12:30 AM, <amber-request.ambermd.org> wrote:
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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Implicit solvent simulation study (Bajarang Kumbhar)
> 2. Re: MCPB and sidechain.bcl problem (Chris Gao)
> 3. Re: Implicit solvent simulation study (Jason Swails)
> 4. Re: Implicit solvent simulation study (Carlos Simmerling)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 24 Aug 2014 11:12:54 +0530
> From: Bajarang Kumbhar <kumbharbajarang.gmail.com>
> Subject: [AMBER] Implicit solvent simulation study
> To: amber.ambermd.org
> Message-ID:
> <CAMvE0Boie=
> FRkQdWbh6Q0ptA-bb6t3ytxE1Z2jHW_5OOrGD2hQ.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> *Dear ALL AMBER USER *
> I want to do simulation of protein using IMPLICIT method and i am new
> regarding this one.
> I have used this protocol for implicit MD*. *
>
> Minimization -> Heating -> Equilibration -> production MD.
>
> *(please help me regarding to setup implicit simulation)*
>
> *I have used this file.........*
>
> *Minimization of protein*
> *&cntrl *
> *imin=1, maxcyc=2000, ncyc=1000, *
> *cut=999.0, **igb=5,ntb=0, *
> *ntc=2,ntf=2, **ntpr=100, *
> *ntr=1, restraintmask=':1-438, *
> *restraint_wt=50.0 *
>
>
>
>
>
>
>
>
>
>
>
> *Heating of system&cntrl imin=0,irest=0,ntx=1, nstlim=100000, dt=0.001,
> ntc=2,ntf=2, cut=999.0, igb=5,ntb=0, ntpr=1000, ntwx=0, ntt=3,
> gamma_ln=2.0, tempi=0.0, temp0=300.0, ntr=1, restraintmask=':1-438',
> restraint_wt=5.0, nmropt=1 / &wt TYPE='TEMP0', istep1=0, istep2=100000,
> value1=0.1, value2=300.0, / &wt TYPE='END' / *
>
> *equilibration file: *
>
> *imin=0,** igb=2, cut=20.0,** ntr=1, intdiel=1.0 , extdiel=78.5, ntb=0,
> nstlim=20000, dt=0.002, ntc=2, ntf=2,*
> * tempi=10.0, temp0=300.0,** ntt=1,** tautp=2.0,** ntp=0,** ntpr=100,
> ntwx=0 *
>
> Thanks
>
> --
>
> *Dr. Bajarang V. Kumbhar* M.Sc.
> Ph.D
> Post-Doctoral Fellow
> Lab-204, Biophysics and Computational Biology,
> Department of Biosciences and Bioengineering,
> Indian Institute of Technology Bombay, Powai Mumbai-400076
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 24 Aug 2014 19:21:10 +0800 (GMT+08:00)
> From: "Chris Gao" <yuhuigao.mail.dlut.edu.cn>
> Subject: Re: [AMBER] MCPB and sidechain.bcl problem
> To: "AMBER Mailing List" <amber.ambermd.org>
> Message-ID:
> <409aec9d.95.14807bf9c33.Coremail.yuhuigao.mail.dlut.edu.cn>
> Content-Type: text/plain; charset=utf-8
>
> Thanks, Pengfei!
>
> I now successfully modify the sidechain.bcl file for my system but new
> questions come that:
>
> The metal Calcium in my protein's active site links with .O.. atom which
> is not on sidechain
>
> so, The sidechain.bcl is that:
>
> # Create bonds with Calcium
> createBond /NAME/CLR/CA1/C0.. /NAME/CLR/AN1/.OD1
> createBond /NAME/CLR/CA1/C0.. /NAME/CLR/VA1/.O.. (VA1=VAL)
> createBond /NAME/CLR/CA1/C0.. /NAME/CLR/TR1/.O.. (TR1=TRP)
>
> that first line OD1 has no problem, but the last two containg .O.. atom
> in backbone. I check the bcl.log file, it says:
>
> ### ### ### ###
> ### MTK++ Info ###
> ### Function: selection::parse ###
> ### Message: selection string = /2xjp/CLR/VA1/.O..
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: selection::parse ###
> ### Message: /col/mol/smol/atom selection error (7) ... exiting
> ### ### ### ###
>
> ### ### ### ###
> ### MTK++ Error ###
> ### Function: MCPB::createBond ###
> ### Message: Error in selection parsing ... exiting
> ### ### ### ###
>
> It seems that sidechain.bcl only pocess metal interacts with sidechain???
> Not atom in backbone??
>
>
> Thanks for your kind help!
>
> Yuhui
>
>
>
> > -----????-----
> > ???: "Pengfei Li" <ambermailpengfei.gmail.com>
> > ????: 2014?8?23? ???
> > ???: "AMBER Mailing List" <amber.ambermd.org>
> > ??:
> > ??: Re: [AMBER] MCPB and sidechain.bcl problem
> >
> > Hi Yuhui,
> >
> > On Aug 22, 2014, at 8:55 AM, ??? <yuhuigao.mail.dlut.edu.cn> wrote:
> >
> > > Hi .all!
> > >
> > > I have some difficulties in MCPB.
> > >
> > > 1st): I edit original my pdb file end run
> > > MCPB 1234_addHs.bcl -l 1234_addHs.bcl.log
> > > but occurs Error: 1 Error in watProtonate ... exiting
> > > terminate called after throwing an instance of 'MTKpp::MTKException'
> > > Aborted (core dumped)
> > >
> > > Then I use tleap to add H
> > >
> >
> > That is right. MCPB may met problem when adding the hydrogens on water.
> Other tools could be used at this situation.
> >
> > > 2nd): the 1AMP_OH_sidechain.bcl in tutorial generated manually has no
> explanation about syntax and meaning in detail,
> > > I don't know how to modify the bcl file precisely for my own system.
> > >
> > > Like a sentence:
> > >
> > > addFragment terminal/CH3 bd /NAME/CLR/HD1-1/.CB. ag
> /NAME/CLR/HD1-1/.CG. tr /NAME/CLR/HD1-1/.ND1 87.0
> > >
> > > what does the sentence mean and 87.0 stand for??
> >
> > In this example we used the methyl group to replace the CA atom in the
> backbone.
> > 87.0 is the dihedral values between the CA, CB, CG and ND1 atoms of that
> residue in the original PDB file.
> > (If you met a negative dihedral value in PDB, you need to change it to
> positive by adding 360 degree in the MCPB script.)
> > The dihedral values may be different for different residues, you need to
> check them manually before setting them in the script.
> >
> > >
> > > I sincerely hope someone can help me!
> > >
> >
> > Sorry for that there is no notes for that part, I will add notes in that
> part in the corresponding file in that tutorial.
> >
> > > Thanks
> >
> > No problem.
> >
> > All the best,
> > Pengfei
> >
> > > _______________________________________________
> > > 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: 3
> Date: Sun, 24 Aug 2014 10:12:27 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Implicit solvent simulation study
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3qSVo4a_Nm9Mrwjg1+T=
> 1KSLuBCqHfTLyJtm7rYgDAc9A.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Sun, Aug 24, 2014 at 1:42 AM, Bajarang Kumbhar <
> kumbharbajarang.gmail.com
> > wrote:
>
> > *Dear ALL AMBER USER *
> > I want to do simulation of protein using IMPLICIT method and i am
> new
> > regarding this one.
> > I have used this protocol for implicit MD*. *
> >
> > Minimization -> Heating -> Equilibration -> production MD.
> >
> > *(please help me regarding to setup implicit simulation)*
> >
> > *I have used this file.........*
> >
> > *Minimization of protein*
> > *&cntrl *
> > *imin=1, maxcyc=2000, ncyc=1000, *
> > *cut=999.0, **igb=5,ntb=0, *
> > *ntc=2,ntf=2, **ntpr=100, *
> > *ntr=1, restraintmask=':1-438, *
> > *restraint_wt=50.0 *
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *Heating of system&cntrl imin=0,irest=0,ntx=1, nstlim=100000, dt=0.001,
> > ntc=2,ntf=2, cut=999.0, igb=5,ntb=0, ntpr=1000, ntwx=0, ntt=3,
> > gamma_ln=2.0, tempi=0.0, temp0=300.0, ntr=1, restraintmask=':1-438',
> > restraint_wt=5.0, nmropt=1 / &wt TYPE='TEMP0', istep1=0, istep2=100000,
> > value1=0.1, value2=300.0, / &wt TYPE='END' / *
> >
> > *equilibration file: *
> >
> > *imin=0,** igb=2, cut=20.0,** ntr=1, intdiel=1.0 , extdiel=78.5, ntb=0,
> > nstlim=20000, dt=0.002, ntc=2, ntf=2,*
> > * tempi=10.0, temp0=300.0,** ntt=1,** tautp=2.0,** ntp=0,** ntpr=100,
> > ntwx=0 *
> >
>
> ?Why are you switching GB models and cutoffs? This is a bad idea generally
> -- you should almost always use the same Hamiltonian for every step of your
> simulation. And ntt=1 is also a bad choice for thermostat in implicit
> solvent. ntt=3 is better.
>
> HTH,
> Jason
> ?
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 24 Aug 2014 11:06:47 -0400
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Subject: Re: [AMBER] Implicit solvent simulation study
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAGk3s-SM+LOxEEZiydGrp08AYOt2_Le0mryzYRvMPdnM1yt=
> Rg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> What is the goal of the simulation? What type of molecule are you
> simulating? Implicit solvents have different strengths and weaknesses and
> which one you choose depends on your goals (the same goes for many other
> options in your simulation, it's why amber has more than 1 choice for many
> settings).
> On Aug 24, 2014 1:43 AM, "Bajarang Kumbhar" <kumbharbajarang.gmail.com>
> wrote:
>
> > *Dear ALL AMBER USER *
> > I want to do simulation of protein using IMPLICIT method and i am
> new
> > regarding this one.
> > I have used this protocol for implicit MD*. *
> >
> > Minimization -> Heating -> Equilibration -> production MD.
> >
> > *(please help me regarding to setup implicit simulation)*
> >
> > *I have used this file.........*
> >
> > *Minimization of protein*
> > *&cntrl *
> > *imin=1, maxcyc=2000, ncyc=1000, *
> > *cut=999.0, **igb=5,ntb=0, *
> > *ntc=2,ntf=2, **ntpr=100, *
> > *ntr=1, restraintmask=':1-438, *
> > *restraint_wt=50.0 *
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *Heating of system&cntrl imin=0,irest=0,ntx=1, nstlim=100000, dt=0.001,
> > ntc=2,ntf=2, cut=999.0, igb=5,ntb=0, ntpr=1000, ntwx=0, ntt=3,
> > gamma_ln=2.0, tempi=0.0, temp0=300.0, ntr=1, restraintmask=':1-438',
> > restraint_wt=5.0, nmropt=1 / &wt TYPE='TEMP0', istep1=0, istep2=100000,
> > value1=0.1, value2=300.0, / &wt TYPE='END' / *
> >
> > *equilibration file: *
> >
> > *imin=0,** igb=2, cut=20.0,** ntr=1, intdiel=1.0 , extdiel=78.5, ntb=0,
> > nstlim=20000, dt=0.002, ntc=2, ntf=2,*
> > * tempi=10.0, temp0=300.0,** ntt=1,** tautp=2.0,** ntp=0,** ntpr=100,
> > ntwx=0 *
> >
> > Thanks
> >
> > --
> >
> > *Dr. Bajarang V. Kumbhar* M.Sc.
> > Ph.D
> > Post-Doctoral Fellow
> > Lab-204, Biophysics and Computational Biology,
> > Department of Biosciences and Bioengineering,
> > Indian Institute of Technology Bombay, Powai Mumbai-400076
> > _______________________________________________
> > 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
>
>
> End of AMBER Digest, Vol 956, Issue 1
> *************************************
>
--
*Dr. Bajarang V. Kumbhar* M.Sc.
Ph.D
Post-Doctoral Fellow
Lab-204, Biophysics and Computational Biology,
Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai Mumbai-400076
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Received on Mon Aug 25 2014 - 00:00:02 PDT
