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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Sep 16 2007 - 06:07:45 PDT
