Dear Jose,
> 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:
oh oh something wrong - better understanding what's is going on ;-)
See
http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
The command (you used):
me8t8=loadmol2 me8t8_Qneutral.mol2
seems correct, but I would use a three character 'variable'; I guess
this 'variable' should match the residue name in the PDB file
(macrostructure).
Then see
http://ambermd.org/doc6/html/AMBER-sh-5.9.html#sh-5.9.43
I wonder if the command (you used):
me8t8=loadoff me8t8.lib
is correct; instead you could try:
loadoff me8t8.lib
edit XXX # 'XXX is written in the off file and I guess this variable
should match the residue name in the PDB file (macrostructure)
-> See
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
# load the three force field libraries for the NALA, ALA and CALA
fragments in the Amber OFF file format
loadoff NALA.off
loadoff ALA.off
loadoff CALA.off
---
I have no idea if this is the answer to your problem; I like x/tLEaP -
but for sure from what I learned if you use x/tLEaP using the
'non-standard' (what does it mean?) way you get side effects such as
these you observed...
If it does not help - I would be glad to look at your data (if you
agree to share them) to understand what is going on... If so - just
send a compressed/archive file to my personal email address. An
external eye can help to detect a non-standard use of LEaP or to find
just another bug.
regards, Francois
> 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
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Received on Thu Aug 22 2013 - 05:30:02 PDT
