From: dimka (newyorkdimka_at_gmail.com)
Date: Wed Jul 25 2007 - 17:03:37 CDT
Hello, I'd like to calculate all-vs-all residue interactions in the protein
with one namd input script.
I took the following approach:
the occupancy column of each residue I set to its residue number, for
example:
...
ATOM 229 N ILE A 14 1.211 -6.588 -2.830 14.00 0.00 A
ATOM 230 HN ILE A 14 1.485 -7.517 -3.066 14.00 0.00 A
...
ATOM 248 SG CYS A 15 -0.264 -3.235 1.107 15.00 0.00 A
ATOM 249 CB CYS A 15 -1.130 -4.800 1.492 15.00 0.00 A
...
ATOM 257 O CYS A 15 -4.457 -4.867 -0.119 15.00 0.00 A
ATOM 258 N ARG A 16 -3.551 -3.216 0.955 16.00 0.00 A
...
then I used the following script to calculate pair-interactions between all
of these groups,
----------------------------------------------------
structure PROT.psf
coordinates initialized.pdb
paraTypeCharmm on
parameters par_all27_prot_lipid_na.inp
numsteps 1
exclude scaled1-4
outputname namd-temp
temperature 0
COMmotion yes
cutoff 12
dielectric 1.0
switchdist 10
pairInteraction on
pairInteractionFile initialized.pdb
pairInteractionCol O
set nres 22
set frames 100
puts "hello"
for {set i 1} { $i <= [expr $nres - 1]} {incr i} {
pairInteractionGroup1 $i
for {set j [expr $i + 1]} {$j <= $nres} {incr j} {
pairInteractionGroup2 $j
coorfile open dcd protein.dcd
set ts 0
for {set ts 0} { $ts <= 100 } {incr ts} {
firstTimestep $ts
puts "ENERGY: $ts $i $j"
run 0
}
coorfile close
}
}
----------------------------------------------------
and I get the following error:
...
TCL: Setting parameter firstTimestep to 100
ENERGY: 100 1 2
TCL: Running for 0 steps
ENERGY: 100 0.0000 0.0000 0.0000
0.0000
-5.1748 -0.8843 0.0000 0.0000 0.0000
-6.0592 0.0000 -6.0592 -6.0592 0.0000
PAIR INTERACTION: STEP: 100 VDW_FORCE: 10.4543 2.4133
3.8586 ELECT_FORCE: 4.9077 0.6330 -5.9402
Info: Closing coordinate file.
TCL: Setting parameter pairInteractionGroup2 to 3
FATAL ERROR: Setting parameter pairInteractionGroup2 from script failed!
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Setting parameter pairInteractionGroup2 from script
failed!
it seems that you cannot redefine the groups after you evaluate the
energies, is that right?
is there a work around this?
dmitry
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