AMBER Archive (2008)

Subject: AMBER: Problems with neglected restaints

From: anna.schrey_at_gmx.de
Date: Tue Mar 18 2008 - 11:40:20 CDT

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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