CCL: Babel problem (?)



 Sent to CCL by: Martin Lindh [martinlindh^_^yahoo.se]
 Thank you for your reply.
 When I have tried to import the sdf files directly
 into Sybyl. I get different atom types than if i first
 convert the files to mol2 format using Babel. For
 example I get the 03 type on charged oxygens in
 phosphate groups instead of 0co2.
 The Babel converted molecules (the one that convert
 well) seem to dock better in FlexX than if I convert
 them by importing them directly into Sybyl.
 I compute charges using the spl script dbcharges so I
 want to be able to import the molecules into Sybyl.
 regards
 Martin
 --- "Cross, Simon scross{=}tripos.com"
 <owner-chemistry::ccl.net> skrev:
 >
 > Sent to CCL by: "Cross, Simon" [scross_-_tripos.com]
 > Martin, I'm not sure what the Babel problem is, but
 > a simple alternative
 > would be to import the SDF directly into the SYBYL
 > spreadsheet. Even
 > simpler would be to select SDF as the ligand input
 > file format from the
 > docking interface.
 >
 > If it is command-line translation you are after,
 > SYBYL's dbtranslate
 > utility should also be available to you.
 >
 > Regards,
 >
 > Simon
 >
 > ------------------------------------
 > Dr Simon Cross
 > Product Manager
 > Tripos UK Ltd
 > scross(!)tripos.com
 > Tel +44 1908 650021
 > Mob +44 7980 572278
 > Fax +44 1908 650001
 > ------------------------------------
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 > -----Original Message-----
 > > From: owner-chemistry(!)ccl.net
 > [mailto:owner-chemistry(!)ccl.net]
 > Sent: Friday, March 16, 2007 5:16 PM
 > To: Cross, Simon
 > Subject: CCL: Babel problem (?)
 >
 >
 > Sent to CCL by: "Martin  Lindh"
 > [martinlindh-$-yahoo.se]
 > Hi
 >
 > I prepare ligands using LigPrep (Maestro). Since I
 > want to dock these
 > ligands
 > in FlexX (Sybyl), I export the ligands from Maestro
 > as a .sdf file. I
 > then
 > use Babel to convert the .sdf file to a multi .mol2
 > file. The .mol2 file
 > is
 > then imported into Sybyl.
 >
 > During this process some(!) of the ligands get
 > strange mol2 formating.
 >
 > Part of a molecule that is translated correctly into
 > the mol2-file:
 > [A]<TRIPOS>ATOM
 > 1 P1    -7.7746    0.3497    0.1484 P.3   	1  <1>
 >      0.1085
 > 2 O1    -7.2207    1.7666   -0.1209 O.2     	1  <1>
 >       -0.4607
 > 3 O2    -7.9571   -0.5515   -1.0931 O.co2   	1  <1>
 >       -0.3575
 >
 > Part of a molecule that is NOT translated correctly
 > in mol2-file:
 >
 > 28 C         14.2736    6.1106   -1.8492 C.ar    0
 > UNK0        0.1493
 > 29 N         14.3973    5.3090   -0.7250 N.ar    0
 > UNK0       -0.2079
 > 30 N         13.7198    8.3248   -1.0353 N.pl3   0
 > UNK0       -0.3413
 > 31 C1*       15.1231    2.8403   -3.4280 C.3     1
 > UNK1        0.1683
 > 32 O4*       15.0326    3.1353   -4.7858 O.3     1
 > UNK1       -0.3456
 > 33 C4*       13.7316    2.8114   -5.2536 C.3     1
 > UNK1        0.1126
 >
 > Anyone seen this problem and have suggestions of
 > what to do?
 >
 > Thank you in advance
 >
 Martinhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp-:-//www.ccl.net/chemistry/sub_unsub.shtmlhttp-:-//www.ccl.net/spammers.txt
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