There's something going on. I get different 'prmtop' files whether I use
the 'mol2' file or the
'
off' file that I derived from the 'mol2' file:
I get one prmtop from this tleap script that uses the 'mol2' file:
source leaprc.ff10
addAtomTypes { { "SI" "Si" "sp3" } }
loadAmberParams mySi.dat
me8t8=loadmol2 me8t8_Qneutral.mol2
saveAmberParm me8t8 my.prmtop my.mdcrd
quit
And I get a different prmtop from these tleap scripts using an 'off'
derived file:
N11 = loadMol2 me8t8_Qneutral.mol2
saveOff N11 me8t8.lib
quit
source leaprc.ff10
addAtomTypes { { "SI" "Si" "sp3" } }
loadAmberParams mySi.dat
me8t8=loadoff me8t8.lib
saveAmberParm me8t8 my.prmtop my.mdcrd
quit
I know these two prmtop files are different by looking at the potentials.
For instance, the first prmtop file contains:
%FLAG
BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
3.40000000E+02 1.89650000E+02 3.50120000E+02
W
hile the second once contains:
%FLAG
BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
3.50120000E+02 3.40000000E+02 1.89650000E+02
Looks like the values are shuffled, but that would imply that the ordering
of the atoms has changed. However, the two prmtop files are indentical when
looking at the %FLAG ATOM_NAME section.
On Wed, Aug 21, 2013 at 6:54 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Jose,
>
> The 'mol2' & 'off' file formats (same remark for the 'prep' one) have
> the same role: a force field library file format. The mol2 format has
> some advantages and the off one other advantages.
> See http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
>
> You might also be intested by the mol3 file format:
> See http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
>
> regards, Francois
>
>
> > I have used a mol2 file to create a topology file with this very simple
> > tleap script:
> >
> > x = loadMol2 mymolecule.mol2
> > saveOff x mymolecule.lib
> > quit
> >
> > I was wondering if there are any sort of internal checks and tools to
> > detect possible errors in file mymolecule.lib
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 21 2013 - 08:30:03 PDT
