CCL: can't open PDB with TINKER GUI

 Sent to CCL by: Paolo Tosco [paolo.tosco++unito.it]
 Dear Steven,
 if MMFF94 atom typing is what you are looking for, you might want to use
 SDF2XYZ2SDF:
 http://sdf2xyz2sdf.sourceforge.net/
 If you look at the examples on the website docs you'll see how to directly
 convert a PDB file to TINKER XYZ. In case of trouble, just drop me an e-mail.
 Cheers,
 Paolo
 --
 ==========================================================
 Paolo Tosco, Ph.D.
 Department of Drug Science and Technology
 Via Pietro Giuria, 9 - 10125 Torino (Italy)
 Tel: +39 011 670 7680 | Mob: +39 348 5537206
 Fax: +39 011 670 7687 | E-mail: paolo.tosco|,|unito.it
 http://open3dqsar.org | http://open3dalign.org
 ==========================================================
 On 13 Sep 2012, at 17:00, "Trohalaki, Steven CTR USAF AFMC AFRL/RXPJE
 Steven.Trohalaki.ctr\a/wpafb.af.mil" <owner-chemistry|,|ccl.net>
 wrote:
 >
 > It appears that the tinker utility pdbxyz.x read the atom names from the
 > Materials Studio PDB file and wrote them to the tinker.xyz file as it.
 This
 > screwed up the formatting (tinker.xyz files are fixed format) because the
 > atom names in the MS PDB contain the atom number, e.g., C123.
 >
 > Using the unix commands cut and paste, I was able to correct the format of
 > my tinker.xyz files.  FFE still wouldn't read it, however, until I replaced
 > the atom types (pdbxyz.x wrote them all as zero) with non-zero integers.
 >
 > Now, I'm trying to use MOLDEN to assign atom types but I'm not having any
 > luck; MOLDEN replaces my non-zero atom-type integers with zeros!  It looks
 > like I'll have to do it manually.  Luckily, I get paid by the hour
 (although
 > maybe not for long).
 >
 > Steve T
 >
 >
 > -----Original Message-----
 >> From: owner-chemistry+steven.trohalaki==wpafb.af.mil-,-ccl.net
 > [mailto:owner-chemistry+steven.trohalaki==wpafb.af.mil-,-ccl.net] On Behalf
 Of
 > Steven Trohalaki steven.trohalaki###wpafb.af.mil
 > Sent: Monday, September 10, 2012 11:39 AM
 > To: Trohalaki, Steven CTR USAF AFMC AFRL/RXPJE
 > Subject: CCL: can't open PDB with TINKER GUI
 >
 >
 > Sent to CCL by: "Steven  Trohalaki"
 [steven.trohalaki[*]wpafb.af.mil]
 >
 > Im trying to import into FFE (TINKERs GUI) a structure I made with
 Materials
 > Studio.
 >
 > I saved the Materials Studio structure as a PDB file.  If I use the TINKER
 > utility pdbxyz.x, I get a tinker.xyz file but when I try to open it in FFE,
 > I get a blank screen and no Structural Hierarchy on the left side of the
 FFE
 > display.  Making up a tinker.key file before I try opening the tinker.xyz
 > file doesnt help.
 >
 > I can open my PDB file directly with FFE.  I am prompted to select a force
 > field, I see a structure, and I see a Structural Hierarchy.  Clicking on
 > Keyword Editor allows me to select keywords and values for the keywords.
 > However, when I click on Modeling Commands, the only commands I see are
 > NUCEIC, PDBXYZ, and PROTEIN, i.e., I dont see Optimize, Dynamics, etc.  I
 do
 > see all of the Modeling Commands if I open one of the example files
 provided
 > for TINKER, e.g., alkane.xyz.
 >
 > Id be obliged if anyone can tell me if Im doing anything wrong or if they
 > have a work-around.
 >
 > Thanks.
 >
 > Steve Thttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp-:-//www.ccl.net/chemistry/sub_unsub.shtmlhttp-:-//www.ccl.net/spammers.txt------=_NextPart_000_0026_01CD9196.8C3D6C50
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