Distinguished Sir or Madam
I'm trying to run minimization and production MD with 6 distance restraint between zinc and six residues. But I found that the distance restraints failed in minimazation and MD.
Here are my input files:
Minimization
&cntrl
imin=1,maxcyc=10000,ncyc=5000,
cut=10,ntb=1,
nmropt=1,
/
&wt type='END'/
LISTONT=POUT
DISANG=dist.RST
MD
&cntrl
imin=0,
nstlim=2500000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=500,ntwx=500,
ntt=3, gamma_ln=2.0
ntb=2, pres0=1.0, ntp=1,taup=2.0,
ntc=2, ntf=2,
cut = 10.0,tempi=298.0,temp0=298.0
ntr=0,
nmropt=1,
/
&wt type='END',/
LISTONT=POUT
DISANG=dist.RST
Harmonic restraints for distance
# some distance constraints
#
# 758 ZNB D1 270 ASP OD2 2.0
&rst
ixpk= 0, nxpk= 0, iat= 11596,4193, r1= 1.60, r2= 1.80, r3= 2.00, r4= 3.00,
rk2=0.0, rk3=132.0, ir6=1, ialtd=0,
&end
#
# 758 ZNB D2 177 ASP OD1 2.2
&rst
ixpk= 0, nxpk= 0, iat= 11597,2776, r1= 1.60, r2= 2.00, r3= 2.20, r4= 3.00,
rk2=0.0, rk3=132.0, ir6=1, ialtd=0,
&end
#
# 758 ZNB D4 179 HIN ND1 2.0
&rst
ixpk= 0, nxpk= 0, iat= 11599,2804, r1= 1.60, r2= 1.80, r3= 2.00, r4= 3.00,
rk2=0.0, rk3=132.0, ir6=1, ialtd=0,
&end
# 757 ZNB D3 652 ASP OD2 2.0
&rst
ixpk= 0, nxpk= 0, iat= 11593,10021, r1= 1.60, r2= 1.80, r3= 2.00, r4= 3.00,
rk2=0.0, rk3=132.0, ir6=1, ialtd=0,
&end
#
# 757 ZNB D2 561 HIN ND1 2.2
&rst
ixpk= 0, nxpk= 0, iat= 11592,8642, r1= 1.60, r2= 2.00, r3= 2.20, r4= 3.00,
rk2=0.0, rk3=132.0, ir6=1, ialtd=0,
&end
#
# 757 ZNB D4 559 ASP OD1 2.0
&rst
ixpk= 0, nxpk= 0, iat= 11594,8614, r1= 1.60, r2= 1.80, r3= 2.00, r4= 3.00,
rk2=0.0, rk3=132.0, ir6=1, ialtd=0,
&end
Here are my output files:
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 0.000 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
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 0.000 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
This problem confused me. I suspected that sander and pmemd read the restraints unsuccessfully, I checked input and restraint files many times, but I didn't find the error. I created a pdb file using the prmtop/inpcrd file, and this pdb file would order the atoms according to prmtop file. The number of the RST files was correspnnding to the number in this pdb.
Could someone help me out of the problem? Any response will be highly appreciated!
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Received on Tue May 07 2019 - 20:00:02 PDT
