From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jul 25 2007 - 20:33:27 CDT
Hi Dmitry,
I don't think there's a work around in one run; you'd be better off
writing a shell script to set up and run each pair separately.
Best,
Peter
dimka wrote:
> 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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