CG parameters from dcd file for protein CG modelling

From: Nicolás Pérez (nicolas.a.perez.barriga_at_gmail.com)
Date: Sun Feb 27 2011 - 13:32:18 CST

Hello NAMD users,

actually i must be make modell of transmembranal receptor (extracellular ligand
receptor, unique transmembranal alpha helix and intracellular segment con
phosphatase activity and phosphorilation activity) and simulate their movements.
The complex receptor BMP(BMP from BONE MORPHOGENIC PROTEIN) have three
representants bmp1a receptor, bmp1b receptor and bmp2 receptor.
For modelling three receptors i use homology modelling with modeller,
building segments that not have three-dimensional representation in
pdb file trasmembranal alpha helix and others segments of the
incomplete receptors.
Since the large size of each receptor approximate 500 aminoacids in
bmp1a, bmp1b and 1000 aminoacids in bmp2, simulate their movements on
water and bilayer enviroment is dificult since the atoms number
exceeds 100000.
I am interested in using CG modelling for make a low resolution model
and use molecular dynamics for simulate the complex in two states
apo-ligand state and bound ligand state, my objective is to compare
principal movements in both states to find some pattern to distinguish
transduction mechanism to signaling intracellular nucleus.
To modelling CG model i must parameterize bonded interactions y i need
a dcd file with the information to make this step, i read sbcg
tutorial but i do not understand how to configurate my conf file to
namd simulation.
I simulate my system in vacuum and my file.conf is next:
#############################################################
## JOB DESCRIPTION ##
#############################################################

# Minimization and Equilibration of
# Ubiquitin in a Water Box

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure bmp1ar_autopsf.psf
coordinates bmp1ar_autopsf.pdb
set temperature 310
set outputname bmp1ar_eq

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

# Integrator Parameters
timestep 10 ;# 1fs/step
rigidBonds none ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100

#############################################################
## EXTRA PARAMETERS ##
#############################################################

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
minimize 10000
reinitvels $temperature

run 25000 ;# 5ps

but i obtaine next message error:

ERROR: Atom 7268 velocity is 847.768 -805.985 100.839 (limit is 1000)
ERROR: Atom 7360 velocity is 149.659 795.183 -676.172 (limit is 1000)
ERROR: Atom 7506 velocity is 763.46 -1332.1 -87.3928 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 4762 velocity is -525.283 525.994 -1267.04 (limit is 1000)
ERROR: Atom 4773 velocity is -313.787 -1177.55 817.456 (limit is 1000)
ERROR: Atom 7950 velocity is -834.749 -723.978 174.839 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 4817 velocity is -1053.16 -400.864 -669.938 (limit is 1000)
ERROR: Atom 4908 velocity is -928.885 -52.1911 795.172 (limit is 1000)
ERROR: Atom 6383 velocity is 687.086 -884.814 -138.113 (limit is 1000)
ERROR: Atom 7406 velocity is -1057.04 30.456 202.158 (limit is 1000)
ERROR: Atom 7408 velocity is 590.278 638.323 -727.819 (limit is 1000)
ERROR: Atom 7742 velocity is -118.878 51.9033 1026.04 (limit is 1000)
ERROR: Atom 7809 velocity is -1248.54 -792.084 -801.911 (limit is 1000)
ERROR: Atom 7891 velocity is -1009.65 -126.636 -149.296 (limit is 1000)
ERROR: Atom 7907 velocity is -1392 593.197 -486.104 (limit is 1000)
ERROR: Atom 5274 velocity is -354.752 -1013.14 550.176 (limit is 1000)
ERROR: Atom 7363 velocity is -921.4 238.968 -636.253 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 6023 velocity is 1029.83 504.012 -419.695 (limit is 1000)
ERROR: Atom 7560 velocity is 427.389 -61.7249 939.146 (limit is 1000)
ERROR: Atom 7564 velocity is -931.961 -395.245 -305.505 (limit is 1000)
ERROR: Atom 7685 velocity is -575.211 -308.375 970.485 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 2926 velocity is 369.526 -1332.79 145.593 (limit is 1000)
ERROR: Atom 3959 velocity is 214.7 -287.435 -1009.79 (limit is 1000)
ERROR: Atom 4051 velocity is 267.03 1200.04 247.626 (limit is 1000)
ERROR: Atom 4102 velocity is 502.673 -11.2304 -969.896 (limit is 1000)
ERROR: Atom 4118 velocity is 434.038 -673.465 796.555 (limit is 1000)
ERROR: Atom 5412 velocity is 420.59 -701.605 -828.589 (limit is 1000)
ERROR: Atom 5417 velocity is 301.05 67.191 1121.14 (limit is 1000)
ERROR: Atom 5488 velocity is -506.93 -154.008 1019.47 (limit is 1000)
ERROR: Atom 5517 velocity is 620.535 1240.64 634.009 (limit is 1000)
ERROR: Atom 5539 velocity is 330.87 -1173 742.007 (limit is 1000)
ERROR: Atom 3955 velocity is 544.362 222.558 1433.51 (limit is 1000)
ERROR: Atom 4944 velocity is -362.674 -771.857 -577.153 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 3894 velocity is -337.347 -752.388 -660.958 (limit is 1000)
ERROR: Atom 3998 velocity is 202.119 750.155 792.192 (limit is 1000)
ERROR: Atom 4005 velocity is 320.915 -600.858 -963.016 (limit is 1000)
ERROR: Atom 5039 velocity is -120.991 801.18 970.11 (limit is 1000)
ERROR: Atom 5088 velocity is 850.484 -168.183 711.437 (limit is 1000)
ERROR: Atom 5147 velocity is -836.959 409.624 1032.6 (limit is 1000)
ERROR: Atom 5171 velocity is 577.51 -231.236 -1238.62 (limit is 1000)
ERROR: Atom 5646 velocity is -1126.26 -442.979 14.7612 (limit is 1000)
ERROR: Atom 5724 velocity is -1564.97 433.054 129.068 (limit is 1000)
ERROR: Atom 5685 velocity is 750.199 606.341 -757.058 (limit is 1000)
ERROR: Atom 3886 velocity is 671.003 -813.911 390.087 (limit is 1000)
ERROR: Atom 6224 velocity is 804.622 856.158 84.3313 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 2749 velocity is 1327.99 511.831 1052.76 (limit is 1000)
ERROR: Atom 2778 velocity is 114.403 -599.888 813.235 (limit is 1000)
ERROR: Atom 2707 velocity is -1095.42 -810.682 1029.72 (limit is 1000)
ERROR: Atom 2745 velocity is -792.262 814.136 -28.7564 (limit is 1000)
ERROR: Atom 3557 velocity is 898.962 -354.431 641.774 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 2864 velocity is 971.767 24.9079 255.781 (limit is 1000)
ERROR: Atom 2865 velocity is -416.161 954.724 407.532 (limit is 1000)
ERROR: Atom 2897 velocity is 190.65 1029.8 584.954 (limit is 1000)
ERROR: Atom 3068 velocity is -671.135 682.444 331.418 (limit is 1000)
ERROR: Atom 3145 velocity is 1553.13 -115.852 -455.127 (limit is 1000)
ERROR: Atom 4205 velocity is 620.795 89.7423 -1025.12 (limit is 1000)
ERROR: Atom 2937 velocity is 1060.44 -834.932 -277.387 (limit is 1000)
ERROR: Atom 2984 velocity is -1291.41 -146.806 -280.843 (limit is 1000)
ERROR: Atom 3528 velocity is -969.376 290.145 -266.834 (limit is 1000)
ERROR: Atom 2371 velocity is -855.649 101.7 696.768 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 3038 velocity is -292.4 -1080.68 434.13 (limit is 1000)
ERROR: Atom 3900 velocity is 48.7037 -599.042 808.221 (limit is 1000)
ERROR: Atom 3986 velocity is -625.01 696.587 -691.872 (limit is 1000)
ERROR: Atom 3975 velocity is 252.321 936.32 684.194 (limit is 1000)
ERROR: Atom 5107 velocity is 359.799 -1318.28 24.9246 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 2534 velocity is -861.604 -11.0607 652.882 (limit is 1000)
ERROR: Atom 2647 velocity is -1107.05 -139.467 616.249 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 2199 velocity is 322.952 1013.86 90.3257 (limit is 1000)
ERROR: Atom 2201 velocity is -771.452 798.39 553.359 (limit is 1000)
ERROR: Atom 2272 velocity is 51.8381 960.481 -637.954 (limit is 1000)
ERROR: Atom 2226 velocity is 884.769 309.194 -394.722 (limit is 1000)
ERROR: Atom 2404 velocity is 904.48 475.74 447.695 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 1908 velocity is -272.465 -956.066 -231.59 (limit is 1000)
ERROR: Atom 1993 velocity is -863.402 -1148.45 1158.04 (limit is 1000)
ERROR: Atom 2012 velocity is -664.817 -870.532 609.209 (limit is 1000)
ERROR: Atom 2050 velocity is -468.466 879.251 110.118 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 1893 velocity is -725.623 -545.033 475.122 (limit is 1000)
ERROR: Atom 1958 velocity is 773.234 749.997 -512.074 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 1816 velocity is -625.444 26.109 800.618 (limit is 1000)
ERROR: Atom 1826 velocity is -1043.26 655.956 -222.083 (limit is 1000)
ERROR: Atom 1842 velocity is 1020.96 224.589 10.6476 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 1370 velocity is -992.094 -321.123 -508.991 (limit is 1000)
ERROR: Atom 1413 velocity is 905.363 -450.254 19.7125 (limit is 1000)
ERROR: Atom 1404 velocity is 390.24 -254.696 -932.788 (limit is 1000)
ERROR: Atom 1405 velocity is -809.323 -600.543 -91.4717 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 1378 velocity is 544.985 -191.405 -1071.97 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 1284 velocity is 837.218 819.429 128.979 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 7196 velocity is -144.564 -1073.99 621.6 (limit is 1000)
ERROR: Atom 7247 velocity is 158.283 842.357 -598.195 (limit is 1000)
ERROR: Atom 7258 velocity is -219.053 -1180.53 142.298 (limit is 1000)
ERROR: Atom 7266 velocity is 764.961 322.637 860.969 (limit is 1000)
ERROR: Atom 6817 velocity is -461.167 727.767 -1016.43 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 7127 velocity is 146.514 985.098 312.086 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 4673 velocity is -663.141 -759.021 -128.632 (limit is 1000)
ERROR: Atom 4694 velocity is -121.134 906.768 476.875 (limit is 1000)
ERROR: Atom 4698 velocity is -522.271 -1028.14 649.62 (limit is 1000)
ERROR: Atom 6566 velocity is 173.679 -46.6701 -1008.11 (limit is 1000)
ERROR: Atom 6596 velocity is 121.576 -968.296 -684.531 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 4608 velocity is 626.593 1469.91 -389.958 (limit is 1000)
ERROR: Atom 4632 velocity is -775.422 -630.512 91.1025 (limit is 1000)
ERROR: Atom 4643 velocity is 403.517 -719.714 718.817 (limit is 1000)
ERROR: Atom 6426 velocity is -146.433 -309.537 1304.24 (limit is 1000)
ERROR: Atom 6485 velocity is 217.864 377.512 -996.554 (limit is 1000)
ERROR: Atom 6549 velocity is 701.889 355.388 -1085.2 (limit is 1000)
ERROR: Atom 6666 velocity is 584.14 714.63 -836.586 (limit is 1000)
ERROR: Atom 6679 velocity is 60.6628 875.279 -683.896 (limit is 1000)
ERROR: Atom 6796 velocity is 528.539 584.534 -744.208 (limit is 1000)
ERROR: Atom 5315 velocity is -178.857 -972.842 174.716 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 5926 velocity is 1084.72 424.411 2.96499 (limit is 1000)
ERROR: Atom 6049 velocity is 171.674 -703.435 -792.938 (limit is 1000)
ERROR: Atom 6068 velocity is -903.224 -584.16 -1043.8 (limit is 1000)
ERROR: Atom 6072 velocity is 922.471 -570.437 31.5543 (limit is 1000)
ERROR: Atom 6414 velocity is 184.127 -327.875 -935.402 (limit is 1000)
ERROR: Atom 6868 velocity is 266.287 -580.884 1413.11 (limit is 1000)
ERROR: Atom 6900 velocity is -12.9513 740.052 715.212 (limit is 1000)
ERROR: Atom 6976 velocity is -174.73 1091.28 -181.604 (limit is 1000)
ERROR: Atom 7000 velocity is -719.737 -1166.02 212.533 (limit is 1000)
ERROR: Atom 7157 velocity is -64.4988 -198.948 -1091.31 (limit is 1000)
ERROR: Atom 6354 velocity is -853.977 -2283.1 -351.692 (limit is 1000)
ERROR: Atom 7063 velocity is 615.649 -931.614 -234.696 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 3608 velocity is 262.077 -534.651 -923.991 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 3281 velocity is 103.919 -990.106 -491.671 (limit is 1000)
ERROR: Atom 3654 velocity is -557.789 -734.215 1844.49 (limit is 1000)
ERROR: Atom 3656 velocity is 445.99 704.023 -894.3 (limit is 1000)
ERROR: Atom 5381 velocity is -796.758 -33.6031 630.554 (limit is 1000)
ERROR: Atom 3294 velocity is 954.898 647.752 -1874.69 (limit is 1000)
ERROR: Atom 3612 velocity is -205.654 228.764 1235.55 (limit is 1000)
ERROR: Atom 5535 velocity is 308.105 835.371 576.173 (limit is 1000)
ERROR: Atom 3692 velocity is -237.147 1119.26 -854.63 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 3386 velocity is 905.282 326.741 666.064 (limit is 1000)
ERROR: Atom 3708 velocity is -629.768 932.27 246.436 (limit is 1000)
ERROR: Atom 5304 velocity is -897.423 1057.29 -1031.41 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 3262 velocity is -705.84 864.318 514.105 (limit is 1000)
ERROR: Atom 3516 velocity is 662.228 -1011.84 409.614 (limit is 1000)
ERROR: Atom 3590 velocity is 1072.87 291.951 87.2142 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 3215 velocity is -584.376 -804.898 317.302 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 4243 velocity is 638.326 -664.256 -498.832 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 2662 velocity is 863.862 257.005 512.982 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 1611 velocity is 923.769 -416.468 372.498 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 490 velocity is -221.012 -1225.39 47.013 (limit is 1000)
ERROR: Atom 491 velocity is -837.268 809.658 -31.7373 (limit is 1000)
ERROR: Atom 721 velocity is 1149.62 333.632 880.03 (limit is 1000)
ERROR: Atom 756 velocity is -678.231 538.216 810.012 (limit is 1000)
ERROR: Atom 814 velocity is -761.866 112.894 -647.37 (limit is 1000)
ERROR: Atom 1085 velocity is 690.373 883.555 166.731 (limit is 1000)
ERROR: Atom 746 velocity is 790.372 -727.359 595.243 (limit is 1000)
ERROR: Atom 1516 velocity is 583.185 1273.99 688.076 (limit is 1000)
ERROR: Atom 683 velocity is 989.264 851.163 -105.456 (limit is 1000)
ERROR: Atom 1634 velocity is 469.432 -1117.05 -460.414 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 736 velocity is 654.175 1384.39 1268.36 (limit is 1000)
ERROR: Atom 881 velocity is 284.895 -1010.96 18.7329 (limit is 1000)
ERROR: Atom 913 velocity is -244.296 -274.992 -991.858 (limit is 1000)
ERROR: Atom 1420 velocity is -294.987 24.4412 -1018.12 (limit is 1000)
ERROR: Atom 1453 velocity is -360.557 -497.949 -839.13 (limit is 1000)
ERROR: Atom 607 velocity is -334.459 1566.56 697.042 (limit is 1000)
ERROR: Atom 1070 velocity is 319.782 1200.37 -141.365 (limit is 1000)
ERROR: Atom 647 velocity is -191.479 -1001.06 126.445 (limit is 1000)
ERROR: Atom 1619 velocity is -339.711 -900.1 -932.635 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 947 velocity is 324.348 -921.098 768.963 (limit is 1000)
ERROR: Atom 967 velocity is -906.355 459.319 -110.142 (limit is 1000)
ERROR: Atom 991 velocity is -371.005 1243.28 -944.318 (limit is 1000)
ERROR: Atom 1012 velocity is -1117.47 -1136.49 11.2723 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 35 velocity is -281.704 -440.531 1870.36 (limit is 1000)
ERROR: Atom 70 velocity is 375.49 -131.123 958.173 (limit is 1000)
ERROR: Atom 71 velocity is -1339.24 339.817 -371.668 (limit is 1000)
ERROR: Atom 94 velocity is -731.803 -657.892 -305.573 (limit is 1000)
ERROR: Atom 137 velocity is 1309.26 181.369 614.361 (limit is 1000)
ERROR: Atom 260 velocity is 840.568 665.746 733.192 (limit is 1000)
ERROR: Atom 276 velocity is 69.7647 -427.011 -924.838 (limit is 1000)
ERROR: Atom 330 velocity is 677.079 -421.858 -864.522 (limit is 1000)
ERROR: Atom 414 velocity is 570.141 -149.369 -875.7 (limit is 1000)
ERROR: Atom 459 velocity is -850.196 -654.524 -3.40903 (limit is 1000)
ERROR: Atom 1151 velocity is -866.297 673.887 59.877 (limit is 1000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Exiting prematurely.

What conditions i must set up in order to simulate and extract data to
parameterize bonded interaction for the CG model, i should use with
solvent water and bilayer in order to simulate my system or i change
conditions for simulation, pressure or others characteristics.

Thanks for any help

Nicolás Pérez Barriga

Estudiante Pregrado
Ingenieria Bioprocesos
Escuela Ingenieria Bioquimica
Pontíficia Universidad Católica de Valparaíso

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