Note: forwarded message attached.
C.Ramakrishnan.
Lecturer - Bioinformatics
SRM Arts & Science College
Kattankulathur - 603203
Contact :
Mobile - 98405 95180
College - 91 44 27454863
Alt.email: ramki.rpcr.gmail.com
__________________________________________________
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attached mail follows:
Sir,
i tried to simulate protein complex with vitamin e using AMBER GB model. In my trajectory the ligand getting unusual conformation. So please guide me for correct result
herewith i have attached the result files for check
input ligand -----> input-vit.pdb
prepin file ------> vit.prepin
frcmod file -------> vit.frcmod
control files
energy minimization --> min.in
equilibration ---> tmp.in
produciton run ----> md.in
xleap log file -------------> leap.log
Thank you very much
With regards
C.Ramakrishnan.
Lecturer - Bioinformatics
SRM Arts & Science College
Kattankulathur - 603203
Contact :
Mobile - 98405 95180
College - 91 44 27454863
Alt.email: ramki.rpcr.gmail.com
__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
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Molecular Dynamics for 1 ns with 2 fs time-step
&cntrl
imin=0
ntc=2, ntf=2,
cut=12.0, igb=2, saltcon=0.2, gbsa=1,
intdiel=1.0, extdiel=78.5,
ntpr=50, ntwx=100,
nstlim=1000000, dt=0.001,
ntt=1, tempi=300.0, temp0=300.0, tautp=1.0,
ntx=5, irest=0, ntb=0,
nscm=1000,
/
minimization
&cntrl
imin=1, maxcyc=500,
cut=300.0, igb=2, saltcon=0.2, gbsa=1,
intdiel=1.0, extdiel=78.5,
ntpr=10, ntx=1, ntb=0,
ntr=1
/
keep all atoms restrained
5.0
RES 1 122
END
END
equilibration
&cntrl
imin=0
ntc=2, ntf=2,
cut=12.0, igb=2, saltcon=0.2, gbsa=1,
intdiel=1.0, extdiel=78.5,
ntpr=50,
nstlim=10000, dt=0.002,
ntt=1, tempi=0.0, temp0=300.0, tautp=1.0,
ntx=1, irest=0, ntb=0,
nscm=1000,
ntr=1
/
keep all atoms restrained
5.0
RES 1 122
END
END
remark goes here
MASS
BOND
cg-c2 625.00 1.307 same as c1-c2
ANGLE
cg-c1-c3 56.400 177.990 same as c1-c1-c3
cg-c2-c2 70.300 121.620 same as c1-c2-c2
c1-cg-c2 60.800 180.000 same as c1-c1-c2
c1-c2-c 67.966 117.825 Calculated with empirical approach
cg-cg-c2 60.800 180.000 same as c1-cg-c2
cg-c2-c1 72.300 116.770 same as c1-c2-c1
DIHE
c1-cg-c2-c2 1 0.000 180.000 2.000 same as X -c1-c2-X
cg-cg-c2-c1 1 0.000 180.000 2.000 same as X -c1-c2-X
IMPROPER
NONBON
0 0 2
This is a remark line
molecule.res
VIT INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 C10 cg M 3 2 1 1.540 111.208 180.000 -0.03698
5 C11 c1 E 4 3 2 1.581 86.374 105.437 -0.09135
6 C3 c2 M 4 3 2 1.571 156.464 -78.224 -0.07051
7 C2 c2 M 6 4 3 1.431 122.890 -28.335 -0.37631
8 C8 c1 E 7 6 4 1.520 119.046 -0.739 0.32624
9 C7 c M 7 6 4 1.434 119.695 179.985 0.61333
10 O2 o E 9 7 6 1.467 114.600 -177.639 -0.53039
11 C6 c2 M 9 7 6 1.441 120.444 -0.032 -0.39360
12 C13 c1 E 11 9 7 1.550 123.007 179.269 0.32699
13 C5 c2 M 11 9 7 1.450 119.647 0.069 -0.40100
14 C12 c1 E 13 11 9 1.520 121.577 175.610 0.31087
15 C4 c2 M 13 11 9 1.447 119.075 -0.089 0.33626
16 O1 os M 15 13 11 1.429 121.942 -179.988 -0.36504
17 C9 c3 M 16 15 13 1.517 123.871 -137.657 -0.16752
18 C14 c1 E 17 16 15 1.659 135.819 73.248 0.33901
19 C15 c1 M 17 16 15 1.478 92.875 -148.364 0.01804
20 C16 cg M 19 17 16 1.578 131.803 147.717 -0.09094
21 C17 cg M 20 19 17 1.557 113.335 154.445 -0.03567
22 C18 c2 M 21 20 19 1.634 118.129 166.462 -0.08544
23 C19 c1 E 22 21 20 1.549 94.910 105.095 0.15858
24 C20 c1 M 22 21 20 1.627 140.143 -139.190 -0.04390
25 C21 c1 M 24 22 21 1.586 127.064 154.741 -0.06222
26 C22 c1 M 25 24 22 1.588 117.469 -176.105 -0.18543
27 C23 c2 M 26 25 24 1.626 117.871 -177.799 -0.02929
28 C1 c1 E 27 26 25 1.495 99.716 60.351 0.35188
29 C24 c1 M 27 26 25 1.558 115.858 178.171 -0.04125
30 C25 c1 M 29 27 26 1.629 112.801 176.882 0.03335
31 C26 c1 M 30 29 27 1.609 117.572 -178.293 -0.11561
32 C27 c2 M 31 30 29 1.544 132.141 -115.920 -0.45571
33 C29 c1 E 32 31 30 1.541 109.318 -147.101 0.38158
34 C28 c1 M 32 31 30 1.555 110.681 92.381 0.38203
LOOP
C9 C11
C4 C3
IMPROPER
C4 C2 C3 C10
C8 C3 C2 C7
C6 C2 C7 O2
C13 C5 C6 C7
C12 C6 C5 C4
C5 C3 C4 O1
C19 C20 C18 C17
C22 C1 C23 C24
C26 C29 C27 C28
DONE
STOP
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Received on Wed Nov 07 2007 - 06:07:35 PST
