AMBER Archive (2009)

Subject: RE: [AMBER] Equilibration step

From: Olotu Odunayo (paxoo_at_nottingham.ac.uk)
Date: Thu Jul 23 2009 - 01:52:50 CDT

I sent my .frcmod and .prepin files earlier.

These are the last lines of my leap.log file when I was building my topology file.

Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.

** Warning: No sp2 improper torsion term for C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** Warning: No sp2 improper torsion term for NF-CF-CJ-HI
        atoms are: N6 C20 C21 H81
 ** Warning: No sp2 improper torsion term for CI-CJ-CF-HI
        atoms are: C19 C21 C20 H89
 ** Warning: No sp2 improper torsion term for CF-CF-CI-HI
        atoms are: C17 C20 C19 H90
 ** Warning: No sp2 improper torsion term for CF-NE-CE-OE
        atoms are: C17 N7 C18 O14
 ** Warning: No sp2 improper torsion term for CJ-CE-CF-CI
        atoms are: C16 C18 C17 C19
 ** Warning: No sp2 improper torsion term for NF-CF-CJ-HI
        atoms are: N6 C17 C16 H92
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N1 C7 C10 N5
 ** Warning: No sp2 improper torsion term for NB-CB-CB-CA
        atoms are: N2 C10 C7 C8
old PREP-specified impropers:
 <Q56 271>: C15 C3 N19 C18
 <Q56 271>: C16 N19 C15 O38
 <Q56 271>: C17 N35 C33 O37
 <Q56 271>: C33 C29 N35 H22
 <Q56 271>: C28 C24 C29 N35
 <Q56 271>: C29 C27 C28 H21
 <Q56 271>: C28 C26 C27 H20
 <Q56 271>: C27 C25 C26 H19
 <Q56 271>: C26 C24 C25 H18
 <Q56 271>: C29 C25 C24 H17
 total 790 improper torsions applied
 10 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

        res total affected

        CLEU 1
        NDP 1
        NTHR 1
        WAT 7968
  )
 (no restraints)
> exit

                                                              
-----Original Message-----
From: amber-bounces_at_ambermd.org on behalf of Tom Joseph
Sent: Wed 7/22/2009 20:05
To: AMBER Mailing List
Subject: Re: [AMBER] Equilibration step
 
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_at_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_at_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_at_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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