I am suspicious that something is wrong with the starting conformation
of your structure. What is the PDB ID? Were there any missing residues
in the protein structure? Were there any error or warning messages
produced by leap or antechamber? Does "RES 1 270" refer only to the
solute residues, without involving any solvent molecules? As a
starting point, to help isolate the problem, you might try minimizing
and equilibrating just the protein itself, without the ligand, to
avoid worrying about antechamber. Then try again with the ligand and
see where things go wrong.
--Tom
On Wed, Jul 22, 2009 at 12:41 PM, Olotu Odunayo<paxoo.nottingham.ac.uk> wrote:
> I got my protein from the pdb, prepared it standard way
> -changed histidine residues
> - downloaded cofactor NAD+ contributed parameters (Ross Walker)
> - used antechamber to define parameter for my ligand
>
> and minimisation protocol is:
>
> Min of InhA, initial minimisation of solvent + ions
> &cntrl
> imin=1,
> maxcyc=1000,
> ncyc=500,
> ntb=1
> ntr=1
> cut=10.0
> &end
> Hold the Protein fixed
> 500.0
> RES 1 270
> END
> END
>
> and the second step without the restraint.
>
>
>
>
> -----Original Message-----
> From: amber-bounces.ambermd.org on behalf of Tom Joseph
> Sent: Wed 7/22/2009 13:35
> To: AMBER Mailing List
> Subject: Re: [AMBER] Equilibration step
>
> Where did you get your protein and how did you prepare it for
> simulation? Did you minimize your structure (imin=1) before heating?
>
> --Tom
>
> On Wed, Jul 22, 2009 at 5:47 AM, Olotu Odunayo<paxoo.nottingham.ac.uk> wrote:
>> Hi,
>>
>> I am new to molecular simulation, and I am having problems going past the equilibration stage.
>>
>> After equilibration, when I view the average pdb structure, it doesn't look right.
>> 1, RMSD is around 2.75 to 3
>> 2, Some water molecules are skewed together (like having bonds overstretched during minimisation etc)
>>
>> I have tried heat up with restraints, then equilibrating without restraints - some residues of my protein were distorted and I get MPI Quiescence error when i try to do production run
>>
>> I have tried equilibration with restraints and gradually reducing restraints, the pdb actually looks fine but there is large RMSD and bonds in water molecule overstretched.
>>
>> Please can you help, below is a typical input file
>>
>> Heat up
>> 20ps MD with res on protein
>> &cntrl
>> imin = 0,
>> irest = 0,
>> ntx = 1,
>> ntb = 1,
>> cut = 10,
>> ntr = 1,
>> ntc = 2,
>> ntf = 2,
>> tempi = 0.0,
>> temp0 = 300.0,
>> ntt = 3,
>> gamma_ln = 1.0,
>> nstlim = 10000, dt = 0.002,
>> ntpr = 250, ntwx = 250, ntwr = 10000
>> /
>> Keep protein fixed with weak restraints
>> 10.0
>> RES 1 270
>> END
>> END
>>
>> Equilibration
>>
>> Equilibrate density
>> &cntrl
>> imin=0, irest=1, ntx=5,
>> ntb=2, ntp=1, cut=10.0,
>> ntf=2, ntc=2,
>> nstlim=100000, dt=0.002,
>> ntpr=500, ntwx=500,
>> ntr=0,
>> ntt=3, gamma_ln=1., temp0=300.0,
>> /
>>
>> I also tried
>>
>> Heat up to 100
>> Warm it up restraining Protein water and ions free
>> &cntrl
>> imin=0, irest=0, ntx=1,
>> ntb=1, cut=10.0,
>> ntf=2, ntc=2,
>> nstlim=10000, dt=0.002,
>> ntpr=100, ntwx=200,
>> ntr=1,
>> ntt=3, gamma_ln=1., temp0=100.0, tempi=0.0,
>> /
>> Hold Protein fixed
>> 100.0
>> RES 1 270
>> END
>> END
>>
>> Heat to 300
>> MD on water and ions around free raising T to 300K
>> &cntrl
>> nmropt=1,
>> imin=0, irest=1, ntx=5,
>> ntf=2, ntb=2, cut=10.0,
>> ntr=1,
>> nstlim=10000, dt=0.002,
>> ntpr=100, ntwx=200,
>> ntt=3, gamma_ln=1, temp0=300.0, tempi=100.0,
>> ntp=1,
>> ntc=2,
>> &end
>> &wt
>> type='TEMP0', istep1=0, istep2=9999, value1=100.0, value2=300.0
>> &end
>> &wt
>> type='END'
>> &end
>> Hold Protein Fixed
>> 100.0
>> RES 1 270
>> END
>> END
>>
>> Equilibration step reducing restraint by half
>> &cntrl
>> imin=0, irest=1, ntx=5,
>> ntb=2, cut=10.0,
>> ntf=2, ntc=2,
>> nstlim=10000, dt=0.002,
>> ntpr=100, ntwx=200,
>> ntr=1, ntp=1,
>> ntt=3, gamma_ln=1., temp0=300.0,
>> /
>> Hold Protein fixed
>> 50.0
>> RES 1 270
>> END
>> END
>>
>> I reduced to 25.0, 10.0, 5.0, 1.0, then no restraint
>>
>> Thanks
>>
>>
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Received on Wed Jul 22 2009 - 18:07:32 PDT
