Dear all,
I am doing some thermodynamic integration studies on a series of inhibitors (with amber9):
1-I did already the perturbation in solution and it works fine for both the charge and non-bounded
part, so I assume I edited correctly the force field parameters and that the input file for the
TI is correct.
2-The equilibration of the complex seems to be ok, more than 1 ns
3-The perturbation in the complex gives the error vlimit exceeded already in the charge perturbation.
I tried with lambda=0.00001 and already the error occurs. What seems wired to me is that in
solution everything goes fine... the equilibration, the force field parameters of the ligand and
the input perl script for the TI are the same for the solution mutation and the mutation of the
inhibitor in the complex.
Here is the input perl script:
#!/usr/bin/perl -w
.clambda=( 0.00001 );
foreach $in ( 0 .. 0 ){
$out = $in + 1;
#------------------------------------------------------------------------------------------------
# equilibration:
open( MDIN, ">mdin");
print MDIN <<EOF;
charge equilibration
&cntrl
ntr=0,
nstlim=50000,
dt=0.001,
nscm=2000,
ntave=5000,
ntx=7,
irest=1,
ntb=2,
ntp=1,
taup=1.0,
temp0=300.0,
tempi=300.0,
nrespa=1,
ntt=1,
tautp=2.0,
ntc=2,
ntf=2,
tol=0.000001,
ntpr=100,
ntwr=10000,
ntwx=0,
icfe=2,
clambda=${clambda[$in]},
klambda=6,
cut=10.0
/
EOF
close MDIN;
open( GFILE, ">gfile");
print GFILE <<EOF;
-O -i mdin -p complesso.prmtop -c ti_pr_$in.restrt -o ti_eq_$out.out -r ti_eq_$out.restrt -inf mdinfo_eq$out
-O -i mdin -p complesso_cg.prmtop -c ti_pr_$in.restrt -o b_ti_eq_$out.out -r b_ti_eq_$out.restrt -inf b_mdinfo_eq$out
EOF
close GFILE;
system("mpirun C /usr/local/amber9_parallel/exe/sander.MPI -ng 2 -groupfile gfile" );
#-------------------------------------------------------------------------------------------------------------------
# production:
open( MDIN, ">mdin");
print MDIN <<EOF;
perturbate charge
&cntrl
ntr=0,
nstlim=100000,
dt=0.001,
nscm=2000,
ntave=5000,
ntx=7,
irest=1,
ntb=1,
ntp=0,
taup=2.0,
temp0=300.0,
tempi=300.0,
nrespa=2,
ntt=0,
tautp=2.0,
ntc=2,
ntf=2,
tol=0.000001,
ntpr=100,
ntwr =10000,
ntwx=0,
icfe=2,
clambda=${clambda[$in]},
klambda=6,
cut=10.0
/
EOF
close MDIN;
open( GFILE, ">gfile");
print GFILE <<EOF;
-O -i mdin -p complesso.prmtop -c ti_eq_$out.restrt -o ti_pr_$out.out -r ti_pr_$out.restrt -inf mdinfo_pr$out
-O -i mdin -p complesso_cg.prmtop -c ti_eq_$out.restrt -o b_ti_pr_$out.out -r b_ti_pr_$out.restrt -inf 1_mdinfo_pr$out
EOF
close GFILE;
system("mpirun C /usr/local/amber9_parallel/exe/sander.MPI -ng 2 -groupfile gfile" );
}
The errors start here:
------------------------------------------------------------------------------
NSTEP = 1900 TIME(PS) = 1220.900 TEMP(K) = 301.03 PRESS = 61.0
Etot = -97691.6160 EKtot = 25207.5018 EPtot = -122899.1178
BOND = 809.0032 ANGLE = 2329.3973 DIHED = 2685.0068
1-4 NB = 992.8165 1-4 EEL = 11154.6095 VDWAALS = 14937.8572
EELEC = -155807.8082 EHBOND = 0.0000 RESTRAINT = 0.0000
DV/DL = 0.0000
EKCMT = 10909.7551 VIRIAL = 10368.6307 VOLUME = 410522.0438
Density = 1.0178
Ewald error estimate: 0.7471E-04
------------------------------------------------------------------------------
check COM velocity, temp: 0.000000 0.00(Removed)
NSTEP = 2000 TIME(PS) = 1221.000 TEMP(K) = 301.85 PRESS = -260.6
Etot = -97693.7162 EKtot = 25276.4635 EPtot = -122970.1797
BOND = 839.9138 ANGLE = 2226.4346 DIHED = 2678.4856
1-4 NB = 1016.1250 1-4 EEL = 11230.5164 VDWAALS = 14413.8554
EELEC = -155375.5104 EHBOND = 0.0000 RESTRAINT = 0.0000
DV/DL = 0.0000
EKCMT = 10974.2560 VIRIAL = 13284.6302 VOLUME = 410617.7306
Density = 1.0176
Ewald error estimate: 0.6041E-05
------------------------------------------------------------------------------
vlimit exceeded for step 2028; vmax = 620.7118
vlimit exceeded for step 2029; vmax = 24.0966
vlimit exceeded for step 2030; vmax = 28.5528
vlimit exceeded for step 2031; vmax = 21.4656
vlimit exceeded for step 2071; vmax = 376.9714
and finish here
NSTEP = 2600 TIME(PS) = 1221.600 TEMP(K) = 439.86 PRESS = 245.7
Etot = -74599.1614 EKtot = 36833.0544 EPtot = -111432.2158
BOND = 5744.4339 ANGLE = 7002.7115 DIHED = 3186.0220
1-4 NB = 1567.4336 1-4 EEL = 11045.9186 VDWAALS = 15174.6991
EELEC = -155153.4344 EHBOND = 0.0000 RESTRAINT = 0.0000
DV/DL = 0.0000
EKCMT = 11283.3572 VIRIAL = 9101.7085 VOLUME = 411268.0761
Density = 1.0160
Ewald error estimate: 0.1096E-03
------------------------------------------------------------------------------
vlimit exceeded for step 2600; vmax = 31.3998
vlimit exceeded for step 2601; vmax = 20.7354
vlimit exceeded for step 2602; vmax = 59.0127
vlimit exceeded for step 2603; vmax = 193.5040
vlimit exceeded for step 2604; vmax = 27.2560
vlimit exceeded for step 2605; vmax = 21.0932
vlimit exceeded for step 2606; vmax = 101.4387
vlimit exceeded for step 2607; vmax = 20.8958
vlimit exceeded for step 2608; vmax = 25.5303
vlimit exceeded for step 2609; vmax = 38.8451
vlimit exceeded for step 2610; vmax = 35.8532
vlimit exceeded for step 2611; vmax = 31.8020
vlimit exceeded for step 2612; vmax = 23.6545
vlimit exceeded for step 2613; vmax = 21.3717
vlimit exceeded for step 2614; vmax = 23.6274
vlimit exceeded for step 2615; vmax = 21.0513
vlimit exceeded for step 2616; vmax = 21.7138
vlimit exceeded for step 2617; vmax = 98.8253
vlimit exceeded for step 2618; vmax = 26.3571
vlimit exceeded for step 2619; vmax = 21.5356
vlimit exceeded for step 2620; vmax = 48.9072
vlimit exceeded for step 2621; vmax = 27.3903
vlimit exceeded for step 2622; vmax = 27.3654
vlimit exceeded for step 2623; vmax = 38.5152
vlimit exceeded for step 2624; vmax = 32.9717
vlimit exceeded for step 2625; vmax = 20.9460
vlimit exceeded for step 2626; vmax = 29.9075
vlimit exceeded for step 2627; vmax = 22.9752
vlimit exceeded for step 2628; vmax = 25.1487
vlimit exceeded for step 2629; vmax = 87.3217
vlimit exceeded for step 2630; vmax = 27.5888
vlimit exceeded for step 2631; vmax = 21.9951
vlimit exceeded for step 2632; vmax = 20.4515
vlimit exceeded for step 2633; vmax = **********
vlimit exceeded for step 2634; vmax = 28.6393
vlimit exceeded for step 2635; vmax = 60.7355
vlimit exceeded for step 2636; vmax = 30.1171
vlimit exceeded for step 2637; vmax = 56.3720
vlimit exceeded for step 2638; vmax = 147.0185
vlimit exceeded for step 2639; vmax = 21.8624
vlimit exceeded for step 2640; vmax = 20.6548
vlimit exceeded for step 2641; vmax = 24.4316
vlimit exceeded for step 2642; vmax = 61.4618
vlimit exceeded for step 2643; vmax = 23.9325
vlimit exceeded for step 2644; vmax = 25.7458
vlimit exceeded for step 2645; vmax = 39.7429
vlimit exceeded for step 2646; vmax = 25.4819
vlimit exceeded for step 2647; vmax = 22.0230
vlimit exceeded for step 2648; vmax = 23.8011
vlimit exceeded for step 2649; vmax = 22.2173
vlimit exceeded for step 2650; vmax = 20.7662
vlimit exceeded for step 2651; vmax = 21.3147
vlimit exceeded for step 2652; vmax = 25.4589
vlimit exceeded for step 2653; vmax = 22.5790
vlimit exceeded for step 2654; vmax = 29.3044
vlimit exceeded for step 2655; vmax = 91.1247
vlimit exceeded for step 2656; vmax = 66.7892
vlimit exceeded for step 2657; vmax = 30.2612
vlimit exceeded for step 2658; vmax = 24.9777
vlimit exceeded for step 2659; vmax = 23.2033
vlimit exceeded for step 2660; vmax = 68.5263
vlimit exceeded for step 2661; vmax = 21.8420
vlimit exceeded for step 2662; vmax = 20.0989
vlimit exceeded for step 2665; vmax = 28.3789
vlimit exceeded for step 2666; vmax = 20.0267
vlimit exceeded for step 2667; vmax = 23.4509
vlimit exceeded for step 2669; vmax = 21.6286
vlimit exceeded for step 2670; vmax = 21.7316
vlimit exceeded for step 2671; vmax = 20.4000
vlimit exceeded for step 2672; vmax = 27.2242
vlimit exceeded for step 2673; vmax = 39.9073
vlimit exceeded for step 2674; vmax = 52.5959
vlimit exceeded for step 2675; vmax = 49.6837
vlimit exceeded for step 2676; vmax = 470.0263
vlimit exceeded for step 2677; vmax = 467.7807
---------------------------------------
Andrea Bortolato, Ph.D. Student
Molecular Modeling Section
Department of Pharmaceutical Sciences
University of Padova,
Via Marzolo, 5
35131 Padova - ITALY
Phone: +39-049-8275801
Fax: +39-049-8275366 or +39-049-8275704
e-mail:andrea.bortolato.1.unipd.it
Webpage URL
http://mms.dsfarm.unipd.it
----------------------------------------
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Received on Sun Aug 27 2006 - 06:07:13 PDT
