Dear amber community,
I am runnig a simulated annealing protocol with subsequent minimization on a protein-samall molecule-complex. What I want to do, is using restraints to hold cetrain parts of the simulated ligand in place. I am using sander in AMBER7.
However, I get resulting structures that should strongly violate the restraints, but it seems, they are not processed correctly, although fund in the LISTIN file.
Here come the input files:
*****simulated annealing********:
#
# SARUN1, 10000 steps, dt=0.002, TEMP= 1500 K ----->
&cntrl
imin=0, nmropt=1,
ntpr=1000,ntwr=1000,iwrap=1,ntwx=1000,ntwv=1000,
ntwe=1000,
ntf=2,ntb=0,dielc=1,cut=9,scee=1.2,nsnb=10,tempi=300,
ntr=1,nstlim=50000,dt=0.001,ig=1000,ntt=1,tautp=0.002,
ntc=2,
&end
&wt type='TEMP0',istep1=0,istep2=1000, value1=0.0,
value2=10.0, &end
&wt type='TEMP0',istep1=1001,istep2=3000, value1=10.0,
value2=300.0, &end
&wt type='TEMP0',istep1=3001,istep2=5000, value1=300.0,
value2=1500.0, &end
&wt type='TEMP0',istep1=5001,istep2=25000, value1=1500.0 ,
value2=1500.0, &end
&wt type='TEMP0',istep1=25001,istep2=50000,value1=0.0,
value2=0.0, &end
&wt type='TAUTP', istep1=0, istep2=25000,value1=0.002,
value2=0.002, &end
&wt type='TAUTP', istep1=25001,istep2=40000,value1=4.0,
value2=4.0, &end
&wt type='TAUTP', istep1=40001,istep2=45000,value1=4.0,
value2=0.4, &end
&wt type='TAUTP', istep1=45001,istep2=50000,value1=0.4,
value2=0.04, &end
&wt type='REST',istep1=0,istep2=10000,value1=0.01,
value2=0.1, &end
&wt type='REST',istep1=10001,istep2=20000, value1=0.1,
value2=1.0, &end
&wt type='REST',istep1=20001,istep2=50000, value1=1.0,
value2=1.0, &end
&wt type='END' &end
LISTIN=SARUN1.restraints
LISTOUT=SARUN1.violations
DISANG=lgr7.rst
Positional restraints on TM domains
100
FIND
CA * * *
SEARCH
RES 1 327
END
END
STOP
**************Minimization protocol********************************
cat << eof > min1.in
# MINRUN3 after the SA-Run, 10000 steps, full conjugate gradient,after nonbonded pairlist
# upgrade (all 25 steps) 10 steps steepest descent
&cntrl
imin=1, scee=1.2,
ntpr=100, maxcyc=10000,
cut=8.0,
dielc=1,
nsnb=10, ntr=1, drms=1,
ntmin=0, ncyc=10, ntb=0,nmropt=1,
&end
&ewald
eedmeth=5
&end
&wt type='END' &end
LISTIN=MINRUN3_1.restraints
LISTOUT=MINRUN3_1.violations
DISANG=lgr7.rst
Positional restraints on TM domains
100
FIND
CA * * *
SEARCH
RES 1 327
END
END
STOP
eof
mpirun -np 4 \
/swx/amber7/exe_mpi_l/sander -i min1.in -o MINRUN3_1.out \
-p SARUN_TEMPLATE.top -ref SARUN3.crd -c SARUN3.crd \
-r MINRUN3_1.crd -inf MINRUN3_2.mdinf
cat << eof > min1.in
# MINRUN3 after the SA-Run, 10000 steps, full conjugate gradient,after nonbonded pairlist
# upgrade (all 25 steps) 10 steps steepest descent
&cntrl
imin=1, scee=1.2,
ntpr=100, maxcyc=10000,
cut=8.0,
dielc=1,
nsnb=10, ntr=1, drms=0.5,
ntmin=0, ncyc=10, ntb=0,nmropt=1,
&end
&ewald
eedmeth=5
&end
&wt type='END' &end
LISTIN=MINRUN3_2.restraints
LISTOUT=MINRUN3_2.violations
DISANG=lgr7.rst
Positional restraints on TM domains
100
FIND
CA * * *
SEARCH
RES 1 327
END
END
STOP
eof
mpirun -np 4 \
/swx/amber7/exe_mpi_l/sander -i min1.in -o MINRUN3_2.out -p SARUN_TEMPLATE.top -ref MINRUN3_1.crd -c MINRUN3_1.crd \
-r MINRUN3_2.crd -inf MINRUN3_2.mdinf
/bin/rm min1.in
cat << eof > min1.in
# MINRUN3 after the SA-Run, 10000 steps, full conjugate gradient,after nonbonded pairlist
# upgrade (all 25 steps) 10 steps steepest descent
&cntrl
imin=1, scee=1.2,
ntpr=100, maxcyc=10000,
cut=8.0,
dielc=1,
nsnb=10, ntr=1, drms=0.1,
ntmin=0, ncyc=10, ntb=0,nmropt=1,
&end
&ewald
eedmeth=5
&end
&wt type='END' &end
LISTIN=MINRUN3_3.restraints
LISTOUT=MINRUN3_3.violations
DISANG=lgr7.rst
Positional restraints on TM domains
100
FIND
CA * * *
SEARCH
RES 1 327
END
END
STOP
eof
mpirun -np 4 \
/swx/amber7/exe_mpi_l/sander -i min1.in -o MINRUN3_3.out -p SARUN_TEMPLATE.top -ref MINRUN3_2.crd -c MINRUN3_2.crd \
-r MINRUN3_3.crd -inf MINRUN3_3.mdinf
/bin/rm min1.in
cat << eof > min1.in
# MINRUN3 after the SA-Run, 10000 steps, full conjugate gradient,after nonbonded pairlist
# upgrade (all 25 steps) 10 steps steepest descent
&cntrl
imin=1, scee=1.2,
ntpr=100, maxcyc=10000,
cut=8.0,
dielc=1,
nsnb=10, ntr=1, drms=0.05,
ntmin=0, ncyc=10, ntb=0,nmropt=1,
&end
&ewald
eedmeth=5
&end
&wt type='END' &end
LISTIN=MINRUN3.restraints
LISTOUT=MINRUN3.violations
DISANG=lgr7.rst
Positional restraints on TM domains
100
FIND
CA * * *
SEARCH
RES 1 327
END
END
STOP
eof
mpirun -np 4 \
/swx/amber7/exe_mpi_l/sander -i min1.in -o MINRUN3.out -p SARUN_TEMPLATE.top -ref MINRUN3_3.crd -c MINRUN3_3.crd \
-r MINRUN3.crd -inf MINRUN3.mdinf
/bin/rm min1.in
*************DISANG FILE (relevant restaints)**********************
# Asn214 CG to Glu123 CD
&rst iat= 1945, 3424, nstep1=1,nstep2=100000,
r1=0.0,r2=0.0,r3=5.7,r4=5.7,
rk2=50.0, rk3=50.0,
&end
## APY C to Lys274
&rst iat= 274, 329, iresid=1, nstep1=1,nstep2=100000,
r1=0.0,r2=0.0,r3=4.8,r4=4.8,
rk2=50, rk3=50, ialtd=0,
atnam(1)='NZ', atnam(2)='C',
&end
## APY N to Glu123 CD
&rst iat= 123, 329, iresid=1, nstep1=1,nstep2=100000,
r1=0.0,r2=0.0,r3=4.8,r4=4.8,
rk2=50, rk3=50, ialtd=0,
atnam(1)='CD', atnam(2)='N',
&end
****************LISTIN file "MINRUN3_1.restraints (relevant part)*********
******
CD ( 1945)-CG ( 3424) NSTEP1= 1 NSTEP2=100000
R1 = 0.000 R2 = 0.000 R3 = 5.700 R4 = 5.700 RK2 = 50.000 RK3 = 50.000
Rcurr: 5.388 Rcurr-(R2+R3)/2: 2.538 MIN(Rcurr-R2,Rcurr-R3): 0.000
******
NZ ( 4430)-C ( 5376) NSTEP1= 1 NSTEP2=100000
R1 = 0.000 R2 = 0.000 R3 = 4.800 R4 = 4.800 RK2 = 50.000 RK3 = 50.000
Rcurr: 17.176 Rcurr-(R2+R3)/2: 14.776 MIN(Rcurr-R2,Rcurr-R3): 12.376
******
CD ( 1945)-N ( 5368) NSTEP1= 1 NSTEP2=100000
R1 = 0.000 R2 = 0.000 R3 = 4.800 R4 = 4.800 RK2 = 50.000 RK3 = 50.000
Rcurr: 16.822 Rcurr-(R2+R3)/2: 14.422 MIN(Rcurr-R2,Rcurr-R3): 12.022
*************************************************************
Meaning, the ligand APY is far beyond the constraints given in the DISANG file!!!!!
*******************LISTOUT file "MINRUN3_1.violations********************
------------------------------------------------------------------------------
Final Restraint Analysis for coords: MINRUN3_1.crd
Restraints, deviations, and energy contributions: pencut = 0.10
------------------------------------------------------------------------------
First atom Last atom curr. value target deviation penalty
------------------------------------------------------------------------------
Total torsion penalty: 0.098
------------------------------------------------------------------------------
**************************************************************************
Meaning: no remarkable violation of the distance restaint
*******************LISTIN file "MINRUN3_2.restraints (relevant part)*******
CD ( 1945)-CG ( 3424) NSTEP1= 1 NSTEP2=100000
R1 = 0.000 R2 = 0.000 R3 = 5.700 R4 = 5.700 RK2 = 50.000 RK3 = 50.000
Rcurr: 5.384 Rcurr-(R2+R3)/2: 2.534 MIN(Rcurr-R2,Rcurr-R3): 0.000
******
NZ ( 4430)-C ( 5376) NSTEP1= 1 NSTEP2=100000
R1 = 0.000 R2 = 0.000 R3 = 4.800 R4 = 4.800 RK2 = 50.000 RK3 = 50.000
Rcurr: 17.178 Rcurr-(R2+R3)/2: 14.778 MIN(Rcurr-R2,Rcurr-R3): 12.378
******
CD ( 1945)-N ( 5368) NSTEP1= 1 NSTEP2=100000
R1 = 0.000 R2 = 0.000 R3 = 4.800 R4 = 4.800 RK2 = 50.000 RK3 = 50.000
Rcurr: 16.816 Rcurr-(R2+R3)/2: 14.416 MIN(Rcurr-R2,Rcurr-R3): 12.016
***************************************************************************
Meaning: the distance of the ligand is STILL beyond the boundaries of the restaint, although this violation was not found after the first minimization step!!!
I am really desperate! What can I do to make this restraint be of value for the whole MD and minimization runs (I also tried a version without definition of NSTEP, but with the same result!)
Thank you in advance,
Anna
--
Dr. Anna Katharina Schrey
Rungestr. 12
D-10179 Berlin
GERMANY
phone +49(0)30 275 601 92
mobile +49(0)174 18 65 323
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Received on Fri Apr 18 2008 - 21:12:03 PDT
