From: Freda Lim (IHPC) (limch_at_ihpc.a-star.edu.sg)
Date: Wed Feb 05 2014 - 00:12:20 CST

Hi,

I have looked up on the format of the .cgc files and have looked at the example .cgc files that comes with VMD.

I tried to use the CG builder modelling extension but failed because of the following error. Would someone advise what could have gone wrong? And how could I construct a .cgc file that actually works?

Thank you.

Error Log:
atomselect: cannot parse selection text: occupancy >= 0 and segid and ( index 0 or { name H11 and resid 1 and resname HEG } or { name C2 and resid 1 and resname HEG } or { name H21 and resid 1 and resname HEG } or { name H22 and resid 1 and resname HEG } or { name C3 and resid 1 and resname HEG } or { name H31 and resid 1 and resname HEG } or { name H32 and resid 1 and resname HEG } )
atomselect: cannot parse selection text: occupancy >= 0 and segid and ( index 0 or { name H11 and resid 1 and resname HEG } or { name C2 and resid 1 and resname HEG } or { name H21 and resid 1 and resname HEG } or { name H22 and resid 1 and resname HEG } or { name C3 and resid 1 and resname HEG } or { name H31 and resid 1 and resname HEG } or { name H32 and resid 1 and resname HEG } )
    while executing
"atomselect $molid "$fullbeadsel""
    (procedure "apply_bead" line 66)
    invoked from within
"apply_bead $cgbead $molid $rcgout"
    (procedure "::cgtools::apply_database" line 26)
    invoked from within
"::cgtools::apply_database $::cggui::currentToCGMol $::cggui::toCGoutpdbfile $::cggui::revcgfile"
    (procedure "::cggui::buildResidueCGExecute" line 43)
    invoked from within
"::cggui::buildResidueCGExecute"
    invoked from within
".cggui.toCGResidueFrame.applyDB invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 24)
    invoked from within
"tk::ButtonUp .cggui.toCGResidueFrame.applyDB"
(command bound to event)

Input pdb:
TITLE Gromacs Runs One Microsecond At Cannonball Speeds
REMARK THIS IS A SIMULATION BOX
CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 O1 HEG 1 21.650 29.320 25.900 1.00 0.00
ATOM 2 H11 HEG 1 21.710 30.050 26.500 1.00 0.00
ATOM 3 C2 HEG 1 22.960 28.820 25.630 1.00 0.00
ATOM 4 H21 HEG 1 23.620 29.120 26.430 1.00 0.00
ATOM 5 H22 HEG 1 23.330 29.280 24.710 1.00 0.00
ATOM 6 C3 HEG 1 22.950 27.270 25.490 1.00 0.00
ATOM 7 H31 HEG 1 22.550 26.840 26.410 1.00 0.00
ATOM 8 H32 HEG 1 22.270 26.990 24.680 1.00 0.00
ATOM 9 O1 EG 2 24.260 26.720 25.240 1.00 0.00
ATOM 10 C2 EG 2 24.290 25.290 25.110 1.00 0.00
ATOM 11 H21 EG 2 23.630 24.990 24.300 1.00 0.00
ATOM 12 H22 EG 2 23.900 24.840 26.030 1.00 0.00
ATOM 13 C3 EG 2 25.720 24.730 24.840 1.00 0.00
ATOM 14 H31 EG 2 26.110 25.170 23.920 1.00 0.00
ATOM 15 H32 EG 2 26.380 25.030 25.650 1.00 0.00
ATOM 16 O1 EGO 3 25.750 23.290 24.720 1.00 0.00
ATOM 17 C2 EGO 3 27.060 22.740 24.470 1.00 0.00
ATOM 18 H21 EGO 3 27.730 23.030 25.280 1.00 0.00
ATOM 19 H22 EGO 3 27.460 23.170 23.550 1.00 0.00
ATOM 20 C3 EGO 3 27.050 21.190 24.340 1.00 0.00
ATOM 21 H31 EGO 3 26.660 20.740 25.250 1.00 0.00
ATOM 22 H32 EGO 3 26.390 20.880 23.530 1.00 0.00
ATOM 23 O4 EGO 3 28.350 20.670 24.090 1.00 0.00
ATOM 24 H41 EGO 3 28.310 19.730 24.020 1.00 0.00
TER
ENDMDL

.cgc file:
CGBEGIN
HEG HEG2 0
HEG O1 0
HEG H11 0
HEG C2 0
HEG H21 0
HEG H22 0
HEG C3 0
HEG H31 0
HEG H32 0
CGEND
CGBEGIN
EG EG2 0
EG O1 0
EG C2 0
EG H21 0
EG H22 0
EG C3 0
EG H31 0
EG H32 0
CGEND
CGBEGIN
EGO EGO2 0
EGO O1 0
EGO C2 0
EGO H21 0
EGO H22 0
EGO C3 0
EGO H31 0
EGO H32 0
EGO O4 0
EGO H41 0
CGEND

Freda LIM, PhD :: Scientist II:: Consumer Care Team :: Department of Materials Science and Engineering :: Institute of High Performance Computing :: Agency for Science, Technology and Research (A*STAR)
1 Fusionopolis Way, #16-16 Connexis, Singapore 138632 :: DID: (65) 6419 1224 :: limch_at_ihpc.a-star.edu.sg<mailto:limch_at_ihpc.a-star.edu.sg>

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