Hi David,
Here's GLD.lib and the pdb:
--------------------------------------------------------------------
!!index array str
"GLD"
!entry.GLD.unit.atoms table str name str type int typex int resx int
flags int seq int elmnt dbl chg
"AU" "AU" 0 1 131075 1 79 0.0
"AU" "AU" 0 2 131075 1 79 0.0
"AU" "AU" 0 3 131075 1 79 0.0
"AU" "AU" 0 4 131075 1 79 0.0
!entry.GLD.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
"AU" "AU" 0 -1 0.0
"AU" "AU" 0 -1 0.0
"AU" "AU" 0 -1 0.0
"AU" "AU" 0 -1 0.0
!entry.GLD.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.GLD.unit.childsequence single int
5
!entry.GLD.unit.connect array int
0
0
!entry.GLD.unit.hierarchy table str abovetype int abovex str belowtype
int belowx
"U" 0 "R" 1
"R" 1 "A" 1
"U" 0 "R" 2
"R" 2 "A" 2
"U" 0 "R" 3
"R" 3 "A" 3
"U" 0 "R" 4
"R" 4 "A" 4
!entry.GLD.unit.name single str
"default_name"
!entry.GLD.unit.positions table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 2.039000 2.039000
2.039000 0.0 2.039000
2.039000 2.039000 0.0
!entry.GLD.unit.residueconnect table int c1x int c2x int c3x int c4x
int c5x int c6x
0 0 0 0 0 0
0 0 0 0 0 0
0 0 0 0 0 0
0 0 0 0 0 0
!entry.GLD.unit.residues table str name int seq int childseq int
startatomx str restype int imagingx
"GLD" 1 2 1 "?" 0
"GLD" 2 2 2 "?" 0
"GLD" 3 2 3 "?" 0
"GLD" 4 2 4 "?" 0
!entry.GLD.unit.residuesPdbSequenceNumber array int
1
2
3
4
!entry.GLD.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.GLD.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
------------------------------------------------------------------------
ATOM 1 AU GLD 1 0.000 0.000 0.000 1.00 0.00
ATOM 2 AU GLD 2 0.000 2.039 2.039 1.00 0.00
ATOM 3 AU GLD 3 2.039 0.000 2.039 1.00 0.00
ATOM 4 AU GLD 4 2.039 2.039 0.000 1.00 0.00
TER
END
----------------------------------------
A couple other things: can you run MD on atoms of an unknown element as far
as Leap is concerned, i.e. a "?" in the "element" column of the edit atoms
table in Xleap, and what is the "unused" column in that table for? I can't
find any rhyme or reason as to why it is designating some atoms as unused.
Thanks so much
-Tim
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Received on Tue May 22 2018 - 16:00:03 PDT
