From: Jan Saam (jan.saam_at_charite.de)
Date: Thu Nov 27 2003 - 02:43:26 CST
Brian,
this happened to me, too. It has been a while ago, but I think the
reason was an incorrect topology definition of a residue patch that I
generated myself. I defined a bond twice, once in the original residue
and once in the patch.
Another typical reaction of namd to that is the detection of margin
violations.
Below is a little script that checks a structure for double defined
bonds.
Good luck,
Jan
--------------------------
Jan Saam
Humboldt-University Berlin
Charité (medical school)
Institute for Biochemisty
Monbijoustr. 2
10117 Berlin
Germany
phone: +49 30 450 528 449
proc checkbonds { sel } {
set indexlist ""
set i 0
set bonds [$sel getbonds]
set index [$sel list]
set molid [$sel molid]
foreach b $bonds {
set compressed [lsort -real -unique $b]
if {[llength $b]!=[llength $compressed]} {
set atom [atomselect $molid "index [lindex index $i]"]
set res [$atom get resname]
set resid [$atom get resid]
set name [$atom get name]
set seg [$atom get segname]
puts "seg $seg: $res$resid $name : $i: $b"
lappend indexlist $i
}
if {! $i%1000} {puts $i}
incr i
}
return $indexlist
}
Am Do, 2003-11-27 um 00.57 schrieb Brian Bennion:
> Hello,
>
> Has anyone seen this error before? My system is quite large but I know
> others have done larger.
> Below is a snippet of the log file.
>
> Brian
>
>
> nfo: ****************************
> Info: STRUCTURE SUMMARY:
> Info: 4877547 ATOMS
> Info: 3251698 BONDS
> Info: 1625849 ANGLES
> Info: 0 DIHEDRALS
> Info: 0 IMPROPERS
> Info: 0 EXCLUSIONS
> Info: 14632638 DEGREES OF FREEDOM
> Info: 1625849 HYDROGEN GROUPS
> Info: TOTAL MASS = 2.92903e+07 amu
> Info: TOTAL CHARGE = 0 e
> Info: *****************************
> Info: Entering startup phase 0 with 749551 kB of memory in use.
> Info: Entering startup phase 1 with 749551 kB of memory in use.
> Info: Entering startup phase 2 with 1054811 kB of memory in use.
> Info: Entering startup phase 3 with 1092919 kB of memory in use.
> Info: PATCH GRID IS 11 (PERIODIC) BY 11 (PERIODIC) BY 11 (PERIODIC)
> Info: REMOVING COM VELOCITY 0.000438623 -0.000183485 0.000199183
> BUG ALERT: Mother atom with hydrogenGroupSize of 0!
> BUG ALERT: NAMD has detected a bug. Please notify namd_at_ks.uiuc.edu.
> BUG ALERT: Mother atom with hydrogenGroupSize of 0!
> BUG ALERT: NAMD has detected a bug. Please notify namd_at_ks.uiuc.edu.
> [0] MPI Abort by user Aborting program !
>
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