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