Dear all:
I want to constraint the distance between four atoms(GLU355 OE1-WAT588 H1,GLU355 OE2-WAT637 H1),so I use the NMR restraint in my mdin file , After minimal the system,I began to heat it to 300K over 6 stages.The strange thing is that the NMR restraint seems only work at first two stages ,when the Tem reach to 300K,the distance is still far.Could someone tell me the reason? Thank you !
My input file:
Stage 1 heating 50 to 100K
&cntrl
imin=0,irest=1,ntx=5,
nstlim=5000,dt=0.001,
ntc=2,ntf=2,
ntt=3,gamma_ln=1.0,
tempi=50.0,temp0=100.0,
ntb=1,cut=8,
nmropt=1,
ntpr=250,ntwx=500,ntwr=500,
/
&wt type='END' ,
/
LISTIN=POUT
LISTOUT=RST.out
DISANG=dis.RST
The dis.RST
#DISTANTENT.FILE
&rst
ixpk= 0, nxpk= 0, iat= 9299, 5551, r1= 0.84, r2= 1.34, r3= 2.34, r4= 2.84, rk2= 25.0, rk3= 25.0, ir6=1,ialtd= 0,
/
&rst
iat= 69425, 5550, r1= 0.84,r2= 1.34, r3= 2.34, r4=2.84,rk2= 25.0,rk3= 25.0,
/
Outputfile:
3. ATOMIC COORDINATES AND VELOCITIES
-------------------------------------------------------------------------------
begin time read from input coords = 5.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
** No weight changes given **
RESTRAINTS:
Requested file redirections:
LISTIN = POUT
LISTOUT = RST.out
DISANG = dis.RST
Restraints will be read from file: dis.RST
Here are comments from the DISANG input file:
#DISTANTENT.FILE
******
H1 ( 9299)-OE2 ( 5551) NSTEP1= 0 NSTEP2= 0
R1 = 0.840 R2 = 1.340 R3 = 2.340 R4 = 2.840 RK2 = 25.000 RK3 = 25.000
Rcurr: 2.272 Rcurr-(R2+R3)/2: 0.432 MIN(Rcurr-R2,Rcurr-R3): 0.000
******
H1 (69425)-OE1 ( 5550) NSTEP1= 0 NSTEP2= 0
R1 = 0.840 R2 = 1.340 R3 = 2.340 R4 = 2.840 RK2 = 25.000 RK3 = 25.000
Rcurr: 2.123 Rcurr-(R2+R3)/2: 0.283 MIN(Rcurr-R2,Rcurr-R3): 0.000
Number of restraints read = 2
Done reading weight changes/NMR restraints
Input file:
Stage 1 heating 150 to 200K
&cntrl
imin=0,irest=1,ntx=5,
nstlim=5000,dt=0.001,
ntc=2,ntf=2,
ntt=3,gamma_ln=1.0,
tempi=150.0,temp0=200.0,
ntb=1,cut=8,
nmropt=1,
ntpr=250,ntwx=500,ntwr=500,
/
&wt type='END' ,
/
lISTIN=POUT
LISTOUT=RST.out
DISANG=dis.RST
Outputfile:
3. ATOMIC COORDINATES AND VELOCITIES
-------------------------------------------------------------------------------
begin time read from input coords = 10.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
** No weight changes given **
RESTRAINTS:
No valid redirection requests found
** No restraint defined **
Done reading weight changes/NMR restraints
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Received on Wed May 05 2010 - 00:30:03 PDT
