I think that r1 should not match r2, and r3 should not match r4.
the r1 and r4 are linear with slopes that match the parabola
at these points, but in your case the slopes are zero.
On Tue, Mar 18, 2008 at 12:40 PM, <anna.schrey.gmx.de> wrote:
> 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
>
> GMX startet ShortView.de. Hier findest Du Leute mit Deinen Interessen!
> Jetzt dabei sein: http://www.shortview.de/?mc=sv_ext_mf.gmx
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Apr 18 2008 - 21:12:03 PDT
