Dear all,
I solved several NMR solution structures on small molecules or
pseudo-peptides using a typical approach proposed in the tutorials
(
http://ambermd.org/tutorials/advanced/tutorial4/). (build the compounds
using Sirius, run antechamber, then a cooking stage to generate a broad
range of starting random conformations, a short minimization stage and
finally a simulated annealing with NMR restraints). During the
calculations on a specific compound, the temperature is not controled
and "vlimit exceeded" errors occured during the SA protocol and the
system blow up for some structures:
NMR restraints: Bond = 45.822 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 1800 TIME(PS) = 10.900 TEMP(K) = 735.86 PRESS
= 0.0
Etot = 492.0374 EKtot = 271.9857 EPtot = 220.0517
BOND = 66.6660 ANGLE = 130.2428 DIHED = 63.1253
1-4 NB = 23.6357 1-4 EEL = -33.5930 VDWAALS =
-7.1191
EELEC = -66.9061 EHBOND = 0.0000 RESTRAINT =
44.0001
EAMBER (non-restraint) = 176.0516
------------------------------------------------------------------------------
NMR restraints: Bond = 44.000 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 1950; vmax = 89.9614
vlimit exceeded for step 1951; vmax = 184.5955
vlimit exceeded for step 1953; vmax = 20.1344
vlimit exceeded for step 1954; vmax = 104.7867
vlimit exceeded for step 1955; vmax = 124.2341
vlimit exceeded for step 1956; vmax = 34.3084
vlimit exceeded for step 1957; vmax = 312.5428
vlimit exceeded for step 1965; vmax = 20.9487
vlimit exceeded for step 1966; vmax = 20.2604
vlimit exceeded for step 1978; vmax = 20.4966
vlimit exceeded for step 1979; vmax = 20.6110
vlimit exceeded for step 1986; vmax = 20.1992
vlimit exceeded for step 1987; vmax = 20.3008
KE Trans = 73.1618 KE Rot = 102.6922 C.O.M. Vel = 0.395962
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 2000 TIME(PS) = 11.000 TEMP(K) = 10363.98 PRESS
= 0.0
Etot = 6214.8087 EKtot = 3830.7109 EPtot = 2384.0979
BOND = 1721.0956 ANGLE = 468.0087 DIHED = 169.5549
1-4 NB = 43.1493 1-4 EEL = -24.5674 VDWAALS =
23.1335
EELEC = -58.7566 EHBOND = 0.0000 RESTRAINT =
42.4798
EAMBER (non-restraint) = 2341.6180
------------------------------------------------------------------------------
NMR restraints: Bond = 42.480 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 2000; vmax = 21.0159
vlimit exceeded for step 2001; vmax = 22.4172
vlimit exceeded for step 2002; vmax = 22.3471
vlimit exceeded for step 2003; vmax = 22.1767
vlimit exceeded for step 2004; vmax = 21.8347
vlimit exceeded for step 2005; vmax = 21.3662
vlimit exceeded for step 2006; vmax = 20.8227
vlimit exceeded for step 2007; vmax = 20.2536
vlimit exceeded for step 2008; vmax = 20.5435
vlimit exceeded for step 2009; vmax = 23.1266
vlimit exceeded for step 2010; vmax = 22.6441
vlimit exceeded for step 2011; vmax = 22.2349
vlimit exceeded for step 2012; vmax = 21.9243
vlimit exceeded for step 2013; vmax = 21.7273
vlimit exceeded for step 2014; vmax = 21.6365
vlimit exceeded for step 2015; vmax = 21.6064
vlimit exceeded for step 2016; vmax = 21.5573
vlimit exceeded for step 2017; vmax = 21.4144
vlimit exceeded for step 2018; vmax = 21.1612
vlimit exceeded for step 2019; vmax = 20.8571
vlimit exceeded for step 2020; vmax = 20.5846
vlimit exceeded for step 2021; vmax = 20.3870
vlimit exceeded for step 2022; vmax = 20.2623
vlimit exceeded for step 2023; vmax = 20.1910
vlimit exceeded for step 2024; vmax = 20.1547
vlimit exceeded for step 2025; vmax = 20.1349
vlimit exceeded for step 2026; vmax = 20.1071
vlimit exceeded for step 2027; vmax = 20.0398
NSTEP = 2200 TIME(PS) = 11.100 TEMP(K) = 7826.16 PRESS
= 0.0
Etot = 4720.8073 EKtot = 2892.6883 EPtot = 1828.1190
BOND = 910.5835 ANGLE = 698.4564 DIHED = 151.8445
1-4 NB = 41.2481 1-4 EEL = -36.5559 VDWAALS =
57.5731
EELEC = -77.0828 EHBOND = 0.0000 RESTRAINT =
82.0521
EAMBER (non-restraint) = 1746.0669
------------------------------------------------------------------------------
NMR restraints: Bond = 82.052 Angle = 0.000 Torsion = 0.000
===============================================================================
vlimit exceeded for step 2367; vmax = 20.7971
vlimit exceeded for step 2368; vmax = 20.0848
vlimit exceeded for step 2380; vmax = 20.9254
It seems to be related to the COOH C-terminal group of this
pseudo-peptide since no error occured when the molecule is COO-
(nevertheless, NMR experiments were recorded in MeOH and this function
is protonated). Do you have any idea? (may be modifying the tautp
parameter...). Thanks.
Regards,
Baptiste
the SA protocol:
simulated annealing protocol, 20 ps
&cntrl
nstlim=20000, pencut=-0.001, nmropt=1,
ntpr=200, ntt=1, ntwx=200,
cut=15.0, ntb=0, vlimit=10,
/
&ewald
eedmeth=5,
/
#
#Simple simulated annealing algorithm:
#
#from steps 0 to 5000: heat the system to 1000K
#from steps 5001-18000: re-cool to low temperatures with long tautp
#from steps 18001-20000: final cooling with short tautp
#
&wt type='TEMP0', istep1=0,istep2=5000,value1=1000.,
value2=1000., /
&wt type='TEMP0', istep1=5001, istep2=18000, value1=1000.0,
value2=100.0, /
&wt type='TEMP0', istep1=18001, istep2=20000, value1=0.0,
value2=0.0, /
&wt type='TAUTP', istep1=0,istep2=5000,value1=0.4,
value2=0.4, /
&wt type='TAUTP', istep1=5001,istep2=18000,value1=4.0,
value2=4.0, /
&wt type='TAUTP', istep1=18001,istep2=19000,value1=1.0,
value2=1.0, /
&wt type='TAUTP', istep1=19001,istep2=20000,value1=0.1,
value2=0.05, /
&wt type='REST', istep1=0,istep2=3000,value1=0.1,
value2=1.0, /
&wt type='REST', istep1=3001,istep2=20000,value1=1.0,
value2=1.0, /
&wt type='END' /
LISTOUT=POUT
DISANG=NMR.dist
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Received on Wed Nov 07 2012 - 01:30:04 PST
