Dear in the AMBER list
I am following the example of the tutorial B1,
for minimization of steps for explicit solvent.
My model follows with its opening lines and even part of the coordinates
I want to pose restrictions.
Follow my MD control file.
However, the calculation does not follow.
I am specifying something wrong or may be due to gaps in the structure?
Best regards
ATOM 1 N ASP A 35 30.004 14.046 18.117 1.00
23.68 N
ATOM 2 CA ASP A 35 29.077 14.186 19.200 1.00
26.16 C
ATOM 3 C ASP A 35 28.643 12.859 19.787 1.00
31.50 C
ATOM 4 O ASP A 35 27.910 12.870 20.790 1.00
29.44 O
ATOM 5 CB ASP A 35 27.878 15.130 18.884 1.00
31.66 C
ATOM 6 CG ASP A 35 26.937 14.688 17.788 1.00
92.98 C
ATOM 7 OD1 ASP A 35 26.956 13.582 17.262 1.00 51.53
O
ATOM 8 OD2 ASP A 35 26.083 15.629 17.469 1.00100.00 O
ATOM 9 N ARG A 36 29.082 11.727 19.192 1.00
17.69 N
ATOM 10 CA ARG A 36 28.680 10.440 19.738 1.00 16.81
C
ATOM 11 C ARG A 36 29.823 9.448 19.795 1.00
13.68 C
ATOM 12 O ARG A 36 30.718 9.476 18.934 1.00
13.18 O
ATOM 13 CB ARG A 36 27.464 9.858 19.007 1.00
18.77 C
ATOM 14 CG ARG A 36 26.124 10.394 19.527 1.00 23.21
C
.
.
.
.
.
.
ATOM 2549 CA SER A 365 42.384 19.480 6.846
1.00100.00 C
ATOM 2550 C SER A 365 43.386 20.591 6.546
1.00100.00 C
ATOM 2551 O SER A 365 43.675 21.460 7.373
1.00100.00 O
ATOM 2552 CB SER A 365 41.360 19.310 5.729 1.00
44.38 C
ATOM 2553 OG SER A 365 40.200 20.052 6.044
1.00100.00 O
ATOM 2554 OXT SER A 365 41.623 18.562 4.679
1.00100.00 O
TER
HETATM 2556 C RES A 369 45.625 -4.541 26.252 1.00
9.80 C
HETATM 2557 O1 RES A 369 44.914 -5.245 26.929 1.00
10.43 O
HETATM 2558 O2 RES A 369 46.905 -4.325 26.448 1.00
12.35 O
HETATM 5213 O HOH A 429 23.199 -2.356 40.265 1.00
24.17 O
HETATM 5214 O HOH A 430 22.529 -2.195 37.374 1.00
20.18 O
HETATM 5215 O HOH A 431 32.798 6.433 15.772 1.00
14.64 O
HETATM 5216 O HOH A 432 32.934 5.783 18.629 1.00
12.53
Minimize
&cntrl
imin=1,
maxcyc=2000,
ncyc=1000,
ntb=1,
igb=0,
ntr=1,
cut=10.0
/
Hold the 1HZY-A fixed
50.0
RES 1 365
END
END
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 1, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 50, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe
= 0
ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 1, ntb = 1, igb = 0, nsnb
= 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
restraint_wt = 0.00000
Energy minimization:
maxcyc = 2000, ncyc = 1000, ntmin = 1
dx0 = 0.01000, drms = 0.00010
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
vdwmeth = 1, eedmeth = 1, netfrc = 0
Box X = 74.682 Box Y = 80.729 Box Z = 79.589
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 80 NFFT2 = 80 NFFT3 = 80
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
defa
----- READING GROUP 1; TITLE:
Hold the 1HZY-A fixed
GROUP 1 HAS HARMONIC CONSTRAINTS 50.00000
GRP 1 RES 1 TO 365
Number of atoms in this group = 5193
----- READING GROUP 2; TITLE:
END
rfree: End of file on unit 5
Marcelo Andrade Chagas, MSc
(PhD student)
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
*
http://lqcmm.qui.ufmg.br/
Departamento de Química da Universidade Federal de Minas Gerais - UFMG
Tel:(31)3409-5776
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Received on Fri Sep 25 2015 - 11:30:04 PDT
