From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Nov 22 2021 - 13:05:40 CST
If I'm not mistaken, this usually means there's a syntax error and NAMD
is interpreting a stray character or variable name as a keyword. I
couldn't say what the problem is without seeing the entire input script.
On 11/22/21 4:58 AM, Diship Srivastava wrote:
> Thanks for the suggestion. Based on your reply I have written an ad
> hoc tcl script for the same purpose (it harmonically constrains the
> com of bilayer and first few non titratable residues of protein ) but
> during run time the script crashes with unknown tcl error. Any help
> regarding this error will be highly appreciated.
>
>
> script snippet :
> tclForces on
> tclForcesScript {
> set k 0.05
> set r0 9.847
>
> # com of bilayer
> set group1 [addgroup {13 143 266 389 519 649 779 909....}]
> # com of amp
> set group2 [addgroup {15367 15369 15381 15382..}]
> print "starting proc"
> print "-------------"
> proc calcforces {} {
> print "inside proc"
> print "changing scope of variables"
> # set change variable
> global group1 group2 k r0
> # load coordinates
> loadcoords c
> # get z coords of both groups
> set r1 [$c(1)]
> set r2 [$c(2)]
> foreach {x1 y1 z1} $r1 {}
> foreach {x2 y2 z2} $r2 {}
> set r_z [expr {$z2-$z1}]
>
> set disp [expr {$r_z-$r0}]
> # optional add energy - will be displayed in MISC
> # addenergy [expr {$k*$disp*$disp/2.0}]
>
> # calculate force
> set force [expr {-$k*$disp}]
>
> addforce $group1 $force
> addforce $group2 [expr {-1.0*$force}]
>
> }
> # close proc calcforces
> # deleting all atomslections
> clearconfig
> }
>
> In logfile the error encountered was :
> Info: Startup phase 10 took 6.5302e-05 s, 324.613 MB of memory in use
> Info: Startup phase 11 took 0.000188028 s, 324.613 MB of memory in use
> LDB: Central LB being created...
> Info: Startup phase 12 took 0.000182779 s, 324.613 MB of memory in use
> Info: CREATING 1104 COMPUTE OBJECTS
> TCL: starting proc
> TCL: -------------
> TCL: parameter unknown for NAMD config parameter
> FATAL ERROR: Unknown Tcl error
>
> On Sat, 20 Nov 2021 at 21:55, Brian Radak <brian.radak_at_gmail.com
> <mailto:brian.radak_at_gmail.com>> wrote:
>
> This is unfortunately an unsolved problem. As you point out - the
> atom indices change during a CpHMD simulation and so the
> selections would need to be updated at each cycle (probably with a
> bit of bookkeeping). One thing that can be exploited is that the
> number of residues does not change, so if it is possible to use
> residue and name based selections, that should work.
>
> In previous work where we used restraints we took advantage of the
> fact that it was only a single residue that was titrating and so
> all indices above the atom sidechain are fixed during the
> simulation (a bit of a hack).
>
> To be honest, it might be easier for someone to implement
> restraints based on a selection syntax rather than solve the
> indexing problem that is specific to CpHMD.
>
> HTH,
>
> BKR
>
>
> On 11/20/21 12:29 AM, Diship Srivastava wrote:
>> Hi,
>> I am currently working on insertion of an antimicrobial peptide
>> (AMP) on bilayer membrane using constant pH MD. I am trying to
>> constrain the center of mass of AMP and membrane, while cphmd is
>> active. Since cphmd doesn't have colvar support and number of
>> atoms during cphmd changes during the run, both colvars and
>> constraints result in fatal error during the job. How can I
>> constrain the com under cphmd conditions?
>>
>> Thanks in advance.
>>
>>
>>
>> --
>> Diship Srivastava
>> SRF
>> Department of Chemistry
>> IIT(ISM) - Dhanbad
>> India
>
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