From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Sun Jan 20 2013 - 16:46:56 CST
We solve the problem due to Wang namd-l entry from 2006, hope that could
be useful to someone else
# Atoms selected for force application
set id1 3079
set grp1 {}
lappend grp1 $id1
set a1 [addgroup $grp1]
set id2 8423
set id3 8425
set id4 8427
set grp2 {}
lappend grp2 $id2
lappend grp2 $id3
lappend grp2 $id4
set a2 [addgroup $grp2]
On 1/20/2013 5:37 PM, Branko wrote:
> 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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