AMBER Archive (2007)

Subject: Re: AMBER: Torsion terms in xleap

From: David A. Case (case_at_scripps.edu)
Date: Fri Sep 14 2007 - 19:44:17 CDT

On Fri, Sep 14, 2007, Lili Peng wrote:
>
> I have a quick question about preparing a mol2 file in antechamber and
> uploading it into xleap. I currently have a mol2 file...

We have again the situation that has come repeatedly in this thread.

Here is a piece of your mol2 file:

--------------------------------------------------------------------------------
# Created by: Discovery Studio
# Creation time: Fri Sep 14 14:30:52 Pacific Daylight Time 2007

@<TRIPOS>MOLECULE
PTX_bristol
  305 311 2 0 0
PROTEIN
USER_CHARGES

@<TRIPOS>ATOM
      1 C 4.9767 9.2895 -6.0259 C.3 1 SUBUNIT 0.0000
      2 O 2.3045 8.4601 -6.0449 O.3 1 SUBUNIT 0.0000
      3 C 4.4176 5.9765 -2.8288 C.3 1 SUBUNIT 0.0000
      4 C 5.3731 6.0295 -4.1040 C.3 1 SUBUNIT 0.0000
      5 C 6.9380 6.0918 -3.7495 C.3 1 SUBUNIT 0.0000
      6 C 7.2825 7.4616 -2.9834 C.3 1 SUBUNIT 0.0000
  .... etc.....
--------------------------------------------------------------------------------

Even though this is indeed a "mol2-format" file, it doesn't do any good to
load this in LEaP. It has no charges, and the atom types are Discovery
Studio atom types (I guess), and are not Amber/gaff atom types. Besides that,
the atoms don't have unique names, which LEaP requires.

LEaP is a lot less smart than you think: it cannot take a mol2 file created by
Discovery Studio and do anything with it.

All of the "smarts" are in antechamber, which knows how to assign Amber/gaff
atom types, how to get atomic charges, and it even knows how to assign unique
names to all the atoms (although names being arbitary, they might not be names
a human would want to see.)

So, you *must* use antechamber to get mol2 files that you plan to load into
LEaP!

I hope this is clearer than last time around....dac

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