From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Sun Jan 20 2013 - 10:37:56 CST
Hi all,
We desperately need way to assign atoms in the section of the tcl script
in correct way:
set id1 [atomid BH 1 N]
and
set id2 [atomid BH 10 NT]
for id1 we enter [atomid A1 202 CA] segment
name/residue number/atom type
but namd cannot find atom:
Reason: FATAL ERROR: atom not found
while executing
"atomid A1 202 CA"
invoked from within
"set id1 [atomid A1 202 CA]"
(file "smd.tcl" line 5)
Charm++ fatal error:
FATAL ERROR: atom not found
while executing
"atomid A1 202 CA"
invoked from within
"set id1 [atomid A1 202 CA]"
(file "smd.tcl" line 5)
All attempt to enter atom number with 'atomnumbers' similar as in ABF
script give same error. Part of our PDB file is enclosed below
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 N GLU A 1 3.265 8.476 38.421 1.00 0.00 A1
ATOM 2 CA GLU A 1 3.758 9.560 39.169 1.00 0.00 A1
ATOM 3 C GLU A 1 3.045 10.973 38.855 1.00 0.00 A1
ATOM 4 O GLU A 1 3.601 11.969 38.464 1.00 0.00 A1
ATOM 5 CB GLU A 1 5.272 9.578 39.159 1.00 0.00 A1
ATOM 6 CG GLU A 1 5.869 9.797 37.745 1.00 0.00 A1
ATOM 7 CD GLU A 1 5.262 8.991 36.591 1.00 0.00 A1
ATOM 8 OE1 GLU A 1 4.965 9.501 35.531 1.00 0.00 A1
ATOM 9 OE2 GLU A 1 5.110 7.817 36.811 1.00 0.00 A1
ATOM 10 H1 GLU A 1 2.301 8.195 38.572 1.00 0.00 A1
ATOM 11 H2 GLU A 1 3.879 7.675 38.558 1.00 0.00 A1
ATOM 12 H3 GLU A 1 3.278 8.827 37.441 1.00 0.00 A1
ATOM 13 HA GLU A 1 3.616 9.347 40.215 1.00 0.00 A1
ATOM 14 HB1 GLU A 1 5.591 8.617 39.487 1.00 0.00 A1
ATOM 15 HB2 GLU A 1 5.684 10.331 39.777 1.00 0.00 A1
ATOM 16 HG1 GLU A 1 5.801 10.853 37.516 1.00 0.00 A1
ATOM 17 HG2 GLU A 1 6.924 9.455 37.750 1.00 0.00 A1
ATOM 18 N GLY A 2 1.763 10.848 39.151 1.00 0.00 A1
ATOM 19 CA GLY A 2 1.006 12.121 38.969 1.00 0.00 A1
ATOM 20 C GLY A 2 0.278 12.240 37.682 1.00 0.00 A1
ATOM 21 O GLY A 2 -0.075 13.305 37.267 1.00 0.00 A1
ATOM 22 H GLY A 2 1.441 9.909 39.382 1.00 0.00 A1
ATOM 23 HA1 GLY A 2 1.667 13.018 39.214 1.00 0.00 A1
ATOM 24 HA2 GLY A 2 0.312 12.075 39.835 1.00 0.00 A1
ATOM 25 N ARG A 3 0.017 11.099 37.013 1.00 0.00 A1
ATOM 26 CA ARG A 3 -0.728 11.129 35.717 1.00 0.00 A1
ATOM 27 C ARG A 3 -1.552 9.880 35.449 1.00 0.00 A1
ATOM 28 O ARG A 3 -2.089 9.738 34.328 1.00 0.00 A1
ATOM 29 CB ARG A 3 0.188 11.350 34.486 1.00 0.00 A1
ATOM 30 CG ARG A 3 0.512 12.790 34.315 1.00 0.00 A1
ATOM 31 CD ARG A 3 1.442 13.093 33.097 1.00 0.00 A1
ATOM 32 NE ARG A 3 2.170 11.926 32.751 1.00 0.00 A1
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