I'm interested in running umbrella sampling calculations, with restraints
on the phi and psi angles of an alanine dipeptide. I first tried file
redirection, as I do with standard pmemd:
-------------------------------------------------------
Amber 14 SANDER 2014
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 14
| Run on 06/02/2015 at 16:50:01
[-O]verwriting output
File Assignments:
| MDIN: 0000_-175_-175_eq.in
| MDOUT: 0000_-175_-175_eq.out
| INPCRD: /home/lchong/lrb36/for_karl/7_eq2_amber/ALA_eq2.rst
| PARM: /home/lchong/lrb36/for_karl/4_convert/ALA.prmtop
| RESTRT: 0000_-175_-175_eq.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: 0000_-175_-175_eq.crd
| MDINFO: mdinfo
|LOGFILE: logfile
Here is the input file:
&cntrl
irest = 1,
ntx = 5,
ig = -1,
dt = 0.001,
nstlim = 200000,
nscm = 1000,
ntr = 0,
iamoeba = 1,
nmropt = 1,
ntb = 2,
ntp = 1,
pres0 = 1.0,
comp = 44.6,
taup = 10.0,
ntt = 3,
temp0 = 298.0,
gamma_ln = 1.0,
ntf = 1,
ntc = 1,
cut = 12.0,
ntpr = 1000,
ntxo = 1,
ntwr = 20000,
ioutfm = 1,
ntwx = 1000,
iwrap = 1,
/
&ewald
ew_type = 0,
order = 5,
nbflag = 1
skinnb = 2.0,
vdwmeth = 1,
ew_coeff = 0.45,
nfft1 = 50,
nfft2 = 50,
nfft3 = 50,
/
&amoeba
amoeba_verbose = 0,
ee_dsum_cut = 7.0,
dipole_scf_tol = 0.01,
dipole_scf_iter_max = 50,
sor_coefficient = 0.75,
ee_damped_cut = 4.5,
do_vdw_taper = 1,
do_vdw_longrange = 1,
/
&wt
type = "REST",
value1 = 1.0,
&end
&wt
type = "END",
&end
DISANG = restraint.in
| INFO: Old style inpcrd file read
| Conditional Compilation Defines Used:
| AMOEBA
| MPI
| FFTW_FFT
| BINTRAJ
| MKL
| Largest sphere to fit in unit cell has radius = 17.182
| New format PARM file being parsed.
| Version = 1.000 Date = 05/19/15 Time = 17:45:06
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 4141 NTYPES = 1 NBONH = 0 MBONA = 0
NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0
NHPARM = 0 NPARM = 0 NNB = 4257 NRES = 1374
NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 0
NUMANG = 0 NPTRA = 0 NATYP = 1 NPHB = 0
IFBOX = 1 NMXRS = 0 IFCAP = 0 NEXTRA = 0
NCOPY = 0
No Amoeba support for file redirections!
Which seemed pretty clear. I then tried moving the text of my restraint.in
file into the main input:
-------------------------------------------------------
Amber 14 SANDER 2014
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 14
| Run on 06/02/2015 at 17:09:28
[-O]verwriting output
File Assignments:
| MDIN: 0000_-175_-175_eq.in_2
| MDOUT: 0000_-175_-175_eq.out
| INPCRD: /home/lchong/lrb36/for_karl/7_eq2_amber/ALA_eq2.rst
| PARM: /home/lchong/lrb36/for_karl/4_convert/ALA.prmtop
| RESTRT: 0000_-175_-175_eq.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: 0000_-175_-175_eq.crd
| MDINFO: mdinfo
|LOGFILE: logfile
Here is the input file:
&cntrl
irest = 1,
ntx = 5,
ig = -1,
dt = 0.001,
nstlim = 200000,
nscm = 1000,
ntr = 0,
iamoeba = 1,
nmropt = 1,
ntb = 2,
ntp = 1,
pres0 = 1.0,
comp = 44.6,
taup = 10.0,
ntt = 3,
temp0 = 298.0,
gamma_ln = 1.0,
ntf = 1,
ntc = 1,
cut = 12.0,
ntpr = 1000,
ntxo = 1,
ntwr = 20000,
ioutfm = 1,
ntwx = 1000,
iwrap = 1,
/
&ewald
ew_type = 0,
order = 5,
nbflag = 1
skinnb = 2.0,
vdwmeth = 1,
ew_coeff = 0.45,
nfft1 = 50,
nfft2 = 50,
nfft3 = 50,
/
&amoeba
amoeba_verbose = 0,
ee_dsum_cut = 7.0,
dipole_scf_tol = 0.01,
dipole_scf_iter_max = 50,
sor_coefficient = 0.75,
ee_damped_cut = 4.5,
do_vdw_taper = 1,
do_vdw_longrange = 1,
/
&wt
type = "REST",
value1 = 1.0,
&end
&rst
iat=1,6,7,8
ifvari=1,
nstep1=0,
r1=-180.0, r2=-150.0, r3=-150.0, r4=180.0,
rk2=8.0, rk3=8.0,
nstep2=50000,
r1a=-180.0, r2a=-175.0, r3a=-175.0, r4a=180.0,
rk2a=8.0, rk3a=8.0,
&end
&rst
iat=1,6,7,8
ifvari=1,
nstep1=50001,
r1=-180.0, r2=-175.0, r3=-175.0, r4=180.0,
rk2=8.0, rk3=8.0,
nstep2=100000,
r1a=-180.0, r2a=-175.0, r3a=-175.0, r4a=180.0,
rk2a=8.0, rk3a=8.0,
&end
&rst
iat=6,7,9,16
ifvari=1,
nstep1=0,
r1=-180.0, r2=-170.0, r3=-170.0, r4=180.0,
rk2=8.0, rk3=8.0,
nstep2=50000,
r1a=-180.0, r2a==-175.0, r3a==-175.0, r4a=180.0,
rk2a=8.0, rk3a=8.0,
&end
&rst
iat=6,7,9,16
ifvari=1,
nstep1=50001,
r1=-180.0, r2==-175.0, r3==-175.0, r4=180.0,
rk2=8.0, rk3=8.0,
nstep2=100000,
r1a=-180.0, r2a==-175.0, r3a==-175.0, r4a=180.0,
rk2a=8.0, rk3a=8.0,
&end
&wt
type = "END",
&end
| INFO: Old style inpcrd file read
| Conditional Compilation Defines Used:
| AMOEBA
| MPI
| FFTW_FFT
| BINTRAJ
| MKL
| Largest sphere to fit in unit cell has radius = 17.182
| New format PARM file being parsed.
| Version = 1.000 Date = 05/19/15 Time = 17:45:06
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 4141 NTYPES = 1 NBONH = 0 MBONA = 0
NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0
NHPARM = 0 NPARM = 0 NNB = 4257 NRES = 1374
NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 0
NUMANG = 0 NPTRA = 0 NATYP = 1 NPHB = 0
IFBOX = 1 NMXRS = 0 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 4 4 4
| Direct force subcell size = 8.5908 8.6472 8.6480
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
ALA peptide AMOEBA ff
General flags:
imin = 0, nmropt = 1
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1000, ntrx = 1, ntwr =
20000
iwrap = 1, ntwx = 1000, ntwv = 0, ntwe =
0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 1, ntb = 2, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 200000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = -1
temp0 = 298.00000, tempi = 0.00000, gamma_ln= 1.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 10.00000
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub =
1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme =
1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 34.363 Box Y = 34.589 Box Z = 34.592
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 50 NFFT2 = 50 NFFT3 = 50
Cutoff= 12.000 Tol =0.186E-14
Ewald Coefficient = 0.45000
Interpolation order = 5
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
ALA peptide AMOEBA ff
begin time read from input coords = 1020.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
Error: Only TEMP0 TYPE is supported by pmemd Amoeba; line:
REST 0 0 1.000000 0.000000 0 0
I don't need the weight to change over the course of the simulation, or
even the changes in the restrained values as I have written in the input
above; is there an alternative syntax I can use to define torsion
restraints with pmemd.amoeba? I spent some time searching but wasn't able
to figure it out on my own.
Thanks,
Karl
On Thu, May 28, 2015 at 12:17 PM, Karl Debiec <ktd3.pitt.edu> wrote:
> Hi all,
>
> Is it possible to apply torsion restraints with pmemd.amoeba, as in pmemd?
> Based on the error output, it looks as if they are not supported, but I'd
> like to double-check.
>
> Thanks,
> Karl Debiec
>
> --
> Karl Debiec
> Graduate Student, Molecular Biophysics & Structural Biology
> University of Pittsburgh
> Chong Group, Department of Chemistry
> Gronenborn Group, Department of Structural Biology
>
--
Karl Debiec
Graduate Student, Molecular Biophysics & Structural Biology
University of Pittsburgh
Chong Group, Department of Chemistry
Gronenborn Group, Department of Structural Biology
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Received on Thu Jun 04 2015 - 09:00:04 PDT
