VMD-L Mailing List

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Wed Sep 23 2009 - 12:22:27 CDT

Hello,

I have a small molecule that i would like to visualize using VMD, the
molecule is in mol2 format. if i view the molecule the double bond is
shown as a single bond. How can i correct this?

In AMBER i can load the *.lib file but i cannot load the *.lib file into
VMD.

Best,
Taufik


!!index array str
 "beg"
!entry.beg.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
 "C1" "C.2" 0 1 131072 1 6 0.380000
 "O11" "O.2" 0 1 131072 2 8 -0.380000
 "C2" "C.3" 0 1 131072 3 6 -0.100000
 "C21" "C.3" 0 1 131072 4 6 -0.300000
 "H211" "H" 0 1 131072 5 1 0.100000
 "H212" "H" 0 1 131072 6 1 0.100000
 "H213" "H" 0 1 131072 7 1 0.100000
 "C22" "C.3" 0 1 131072 8 6 -0.300000
 "H221" "H" 0 1 131072 9 1 0.100000
 "H222" "H" 0 1 131072 10 1 0.100000
 "H223" "H" 0 1 131072 11 1 0.100000
!entry.beg.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
 "C1" "C.2" 0 -1 0.0
 "O11" "O.2" 0 -1 0.0
 "C2" "C.3" 0 -1 0.0
 "C21" "C.3" 0 -1 0.0
 "H211" "H" 0 -1 0.0
 "H212" "H" 0 -1 0.0
 "H213" "H" 0 -1 0.0
 "C22" "C.3" 0 -1 0.0
 "H221" "H" 0 -1 0.0
 "H222" "H" 0 -1 0.0
 "H223" "H" 0 -1 0.0
!entry.beg.unit.boundbox array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.beg.unit.childsequence single int
 2
!entry.beg.unit.connect array int
 3
 1
!entry.beg.unit.connectivity table int atom1x int atom2x int flags
 1 3 1
 1 2 2
 3 4 1
 3 8 1
 4 5 1
 4 6 1
 4 7 1
 8 9 1
 8 10 1
 8 11 1
!entry.beg.unit.hierarchy table str abovetype int abovex str belowtype int belowx
 "U" 0 "R" 1
 "R" 1 "A" 1
 "R" 1 "A" 2
 "R" 1 "A" 3
 "R" 1 "A" 4
 "R" 1 "A" 5
 "R" 1 "A" 6
 "R" 1 "A" 7
 "R" 1 "A" 8
 "R" 1 "A" 9
 "R" 1 "A" 10
 "R" 1 "A" 11
!entry.beg.unit.name single str
 "BEG"
!entry.beg.unit.positions table dbl x dbl y dbl z
 3.214933 0.278008 -8.099325
 2.350808 0.765469 -7.183709
 4.591772 0.471138 -7.934938
 5.034136 -0.159258 -6.647451
 6.018086 -0.024677 -6.530453
 4.546759 0.264689 -5.883849
 4.831984 -1.138299 -6.669297
 4.889342 1.941208 -7.902272
 5.872960 2.080402 -7.787925
 4.590888 2.360555 -8.759554
 4.402031 2.363165 -7.137527
!entry.beg.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
 0 0 0 0 0 0
!entry.beg.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
 "BEG" 1 12 1 "?" 0
!entry.beg.unit.residuesPdbSequenceNumber array int
 0
!entry.beg.unit.solventcap array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.beg.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
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0


@<TRIPOS>MOLECULE
BEG
   11 10 1 0 1
SMALL
USER_CHARGES
@<TRIPOS>ATOM
  1 C1 3.214933 0.278008 -8.099325 C.2 1 BEG 0.3800 ****
  2 O11 2.350808 0.765469 -7.183709 O.2 1 BEG -0.3800 ****
  3 C2 4.591772 0.471138 -7.934938 C.3 1 BEG -0.1000 ****
  4 C21 5.034136 -0.159258 -6.647451 C.3 1 BEG -0.3000 ****
  5 H211 6.018086 -0.024677 -6.530453 H 1 BEG 0.1000 ****
  6 H212 4.546759 0.264689 -5.883849 H 1 BEG 0.1000 ****
  7 H213 4.831984 -1.138299 -6.669297 H 1 BEG 0.1000 ****
  8 C22 4.889342 1.941208 -7.902272 C.3 1 BEG -0.3000 ****
  9 H221 5.872960 2.080402 -7.787925 H 1 BEG 0.1000 ****
 10 H222 4.590888 2.360555 -8.759554 H 1 BEG 0.1000 ****
 11 H223 4.402031 2.363165 -7.137527 H 1 BEG 0.1000 ****
@<TRIPOS>BOND
    1 1 3 1
    2 1 2 1
    3 3 4 1
    4 3 8 1
    5 4 5 1
    6 4 6 1
    7 4 7 1
    8 8 9 1
    9 8 10 1
   10 8 11 1
@<TRIPOS>SUBSTRUCTURE
      1 BEG 1 **** 0 **** ****