AMBER Archive (2008)

Subject: Re: AMBER: Setting GROUP for pmemd

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Oct 30 2008 - 16:56:27 CDT

On Thu, Oct 30, 2008 at 8:29 PM, Robert Duke <rduke_at_email.unc.edu> wrote:
> Send the actual mdin files, along with a description of which did and did
> not work with pmemd vs. sander.MPI. I noted a caps error below in something
> that supposedly worked ("EnD" keyword). Just glancing at the code, I do
> believe the keywords are going to be case-sensitive.
> Regards - Bob Duke

The lower case "n" was a typo here only.

With pmemd (all residues restrained except WAT) worked well:

Steepest descent minimization to
relax water only
&cntrl
  imin=1, maxcyc=10000, ntmin=2,
  cut=10, ntb=1, ntpr=1, ntr=1
/
Keep protein, ligand and POPC fixed
32.0
RES 1 341
END
END

Steepest descent minimization to
relax water and POPC
&cntrl
  imin=1, maxcyc=10000, ntmin=2,
  cut=10, ntb=1, ntpr=1, ntr=1
/
Keep protein and ligand fixed
32.0
RES 79 341
END
END
======================================================

To restrain the polar heads only of POPC during heating (50ps) and
equilibration (600ps in steps) (78 molecules of POPC are present in
the box), I was unable formulate a valid mdin for pmemd. sander.MPI
worked well with:

Heating gradually complex_box with SHAKE and restraints on
complex and polar heads of POPC
 &cntrl
  imin=0,irest=0, ntx=1,
  nstlim=25000, dt=0.002,
  cut=10,ntb=1,
  ntc=2,ntf=2,
  ntpr=500, ntwx=500,
  ntt=3, gamma_ln=2.0,
  tempi=0.0, temp0=300.0,
  ntr=1,
  restraintmask=":79-341 | :POP_at_O2, P1, O3, O4, O1, C15, C11, N, C12, C13, C14"
  restraint_wt=32,
  nmropt=1
 /
  &wt TYPE='TEMP0', istep1=0, istep2=25000,
  value1=0.1, value2=300.0, /
  &wt TYPE='END' /

Equilibration, restraining protein, ligand, and polar heads of POPC
 &cntrl
  imin=0, irest=1, ntx=5,
  nstlim=25000, dt=0.002,
  cut=10, ntb=2, ntp=1, taup=2.0,
  ntc=2, ntf=2,
  ntpr=1000, ntwx=1000,
  ntt=3, gamma_ln=2.0,
  temp0=300.0,
  ntr=1,
  restraintmask=":79-341 | :POP_at_O2, P1, O3, O4, O1, C15, C11, N, C12, C13, C14"
  restraint_wt=32,
 /
=================================

To continue equilibration while restraining the protein and its ligand
only (using the rst file from the last above equilibration), pmemd
failed with:

Equilibration, restraining protein and ligand
 &cntrl
  imin=0, irest=1, ntx=5,
  nstlim=25000, dt=0.002,
  cut=10, ntb=2, ntp=1, taup=2.0,
  ntc=2, ntf=2,
  ntpr=1000, ntwx=1000,
  ntt=3, gamma_ln=2.0,
  temp0=300.0,
  ntr=1,
 /
  Keep protein and ligand restrained
  32.0
  RES 79 341
  END
  END

The full out file reads:

          -------------------------------------------------------
          Amber 10 SANDER 2008
          -------------------------------------------------------

| PMEMD implementation of SANDER, Release 10

| Run on 10/30/2008 at 19:20:59

  [-O]verwriting output

File Assignments:
| MDIN: equil4.in
| MDOUT: equil4.out
| INPCRD: equil3.rst
| PARM: complex_AA1_POP_BOX.prmtop
| RESTRT: equil4.rst
| REFC: equil3.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: equil4.mdcrd
| MDINFO: mdinfo
|LOGFILE: logfile

 Here is the input file:

Equilibration, restraining protein and ligand
 &cntrl
  imin=0, irest=1, ntx=5,
  nstlim=25000, dt=0.002,
  cut=10, ntb=2, ntp=1, taup=2.0,
  ntc=2, ntf=2,
  ntpr=1000, ntwx=1000,
  ntt=3, gamma_ln=2.0,
  temp0=300.0,
  ntr=1,

 /
  Keep protein and ligand restrained
  32.0
  RES 79 341
  END
  END

| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| MPI
| SLOW_NONBLOCKING_MPI
| PUBFFT
| FFTLOADBAL_2PROC
| MKL

| Largest sphere to fit in unit cell has radius = 38.953

| New format PARM file being parsed.
| Version = 1.000 Date = 10/25/08 Time = 00:28:55
| Duplicated 0 dihedrals

| Duplicated 0 dihedrals

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

 getting new box info from bottom of inpcrd

 NATOM = 84578 NTYPES = 19 NBONH = 78494 MBONA = 6046
 NTHETH = 20048 MTHETA = 7395 NPHIH = 33035 MPHIA = 15321
 NHPARM = 0 NPARM = 0 NNB = 174234 NRES = 23681
 NBONA = 6046 NTHETA = 7395 NPHIA = 15321 NUMBND = 65
 NUMANG = 130 NPTRA = 61 NATYP = 46 NPHB = 1
 IFBOX = 1 NMXRS = 134 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Coordinate Index Table dimensions: 18 16 12
| Direct force subcell size = 6.0744 6.3260 6.4921

     BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

General flags:
     imin = 0, nmropt = 0

Nature and format of input:
     ntx = 5, irest = 1, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 1000, ntrx = 1, ntwr = 500
     iwrap = 0, ntwx = 1000, ntwv = 0, ntwe = 0
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0

Potential function:
     ntf = 2, ntb = 2, igb = 0, nsnb = 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 1

Molecular dynamics:
     nstlim = 25000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00200, vlimit = 20.00000

Langevin dynamics temperature regulation:
     ig = 71277
     temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000

Pressure regulation:
     ntp = 1
     pres0 = 1.00000, comp = 44.60000, taup = 2.00000

SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001

| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1

| Energy averages sample interval:
| ene_avg_sampling = 1000

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, netfrc = 1
     Box X = 109.339 Box Y = 101.215 Box Z = 77.906
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 120 NFFT2 = 108 NFFT3 = 80
     Cutoff= 10.000 Tol =0.100E-04
     Ewald Coefficient = 0.27511
     Interpolation order = 4

| PMEMD ewald parallel performance parameters:
| block_fft = 0
| fft_blk_y_divisor = 2
| excl_recip = 0
| excl_master = 0
| atm_redist_freq = 320

    LOADING THE CONSTRAINED ATOMS AS GROUPS

   5. REFERENCE ATOM COORDINATES

    ----- READING GROUP 1; TITLE:
   Keep protein and ligand restrained

     GROUP 1 HAS HARMONIC CONSTRAINTS 32.00000
 GRP 1 RES 79 TO 341
      Number of atoms in this group = 4106
    ----- READING GROUP 2; TITLE:
   END

     GROUP 2 HAS HARMONIC CONSTRAINTS 0.00000

     rfree: End of file on unit 5
============================

francesco

> ----- Original Message ----- From: "Francesco Pietra"
> <chiendarret_at_gmail.com>
> To: "Amber" <amber_at_scripps.edu>
> Sent: Thursday, October 30, 2008 3:10 PM
> Subject: AMBER: Setting GROUP for pmemd
>
>
>> The pdb is
>> RES 1 78 lipid POPC
>>
>> RES 79 340 protein with capping groups (included in numbering)
>>
>> RES 341 ligand
>> ====
>>
>> Input for pmemd to restrain protein ligand and POPC (the other residues
>> are WAT)
>>
>> /
>> Keep ...
>> 32.0
>> RES 1 341
>> END
>> EnD
>>
>> worked fine.
>> =========
>>
>> The I moved to sander.MPI in order to be able to restrain protein,
>> ligand and a part only of lipid. Now back to pmemd to restrain protein
>> and ligand only
>>
>>
>> /
>> Keep ..
>> 32.0
>> RES 79 341
>> END
>> END
>>
>> the out file:
>> LOADING THE CONSTRAINED ATOMS AS GROUPS
>> 5. REFERENCE ATOM AND COORDINATES
>> READING GROUP 1;TITLE:
>> GROUP 1 HAS HARMONIC CONSTRAINTS 32.00000
>> GRP 1 RES 79 TO 341
>> number of atoms ...
>> READING GROUP 2; TITLE:
>> END
>> GROUP 2 HAS HARMONIC CONSTRAINTS 0.00000
>> rfree: End of file on unit 5
>> ====================
>>
>> Thanks a lot for pointing out my mistake.
>>
>> francesco pietra
>> -----------------------------------------------------------------------
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>
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