From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 23 2009 - 13:17:09 CDT

Hi,
  VMD will currently only draw bond orders if you use the "Bonds"
representation. The representation is somewhat unusual in that it
is drawn as concentric cylinders, but give it a try and let me know
if it works for you. We don't presently have a plugin to read any
".lib" files, whatever those are, so I don't have a suggestion for you
there. (what is a .lib file anyway? Does it go with the .mol2 file?)

Cheers,
  John Stone
  johns_at_ks.uiuc.edu

On Wed, Sep 23, 2009 at 02:13:12PM -0400, Taufik Al-Sarraj wrote:
>
> 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 **** ****
>

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078