CCL: Babel problem (?)
- From: Martin Lindh <martinlindh\a/yahoo.se>
- Subject: CCL: Babel problem (?)
- Date: Mon, 19 Mar 2007 16:31:28 +0100 (CET)
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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