On Thu, Oct 30, 2008 at 8:29 PM, Robert Duke <rduke.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.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.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.gmail.com>
> To: "Amber" <amber.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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Received on Fri Oct 31 2008 - 05:11:57 PDT
