Hi Dr. Case,
My apologies for the repeat question :). However, I did try to do the
"pre-processing" of the mol2 file in antechamber before I sent the original
email, but I ran into a problem with loading the prepi file in xleap. So
that's why tried to load the mol2 file directly into xleap. Anyway, my
commands are listed below:
1. Antechamber:
antechamber -fi mol2 -fo ac -i glu4_linear_PTX.mol2 -o
glu4_linear_PTX.ac
antechamber -fi ac -fo prepi -i ANTECHAMBER_BOND_TYPE.AC -o
glu4_linear_PTX.prepi
parmchk -i glu4_linear_PTX.prepi -f prepi glu4_linear_PTX.frcmod
2. xLeap:
source leaprc.gaff
loadamberparams glu4_linear_PTX.frcmod
loadamberparams gaff.dat
loadamberparams parm99.dat
x = loadamberprep glu4_linear_PTX.prepi
....but I just get the comments:
"This is a remark line: LOOP: redundant bond C--C ignored
This is a remark line: LOOP: redundant bond C--C ignored
This is a remark line: LOOP: redundant bond C--C ignored"
and when I try to "edit x", I get the message:
"Creating a new, empty UNIT "x" "
I initially thought this was an error with the Antechamber commands, but
after reading the other replies in this thread, I wonder if the "LOOP
redundant C--C bonds" refer to the benzene rings in my structure, like
Carlos Simmerling suggested about the "existing database by analogy"? What
about the torsions? I've carefully perused the section on antechamber in
the Amber manual, and the closest thing I could find to addressing 3-4
carbon rings are the aromatic bond types using 'am1bcc'. If you could
provide any guidance or point me in the right direction in the manual, that
would be very helpful.
Thanks in advance,
Lili
On 9/14/07, David A. Case <case.scripps.edu > wrote:
>
> 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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Received on Wed Sep 19 2007 - 06:07:27 PDT
