Dear Francesco,
I tested your two sets of data & this is exactly what I told you in my
first email: Antechamber authorizes non-strict mol2 file format. I
think this is potentially buggy if one wants to use the outputs of
Antechamber in other programs.
When your mol2 file format has a residue number = 4, LEaP crashes
(because a patch was not applied; I think you did not applied the
patch suggested by Dr Case).
When your mol2 file has a residue number = 1, LEaP does not crash. I
only loaded gaff and the geometry of PHA is correct (correct in LEaP,
in VMD using the prmtop/inpcrd generated, correct when using ambpdb &
the prmtop/inpcrd generated).
I did not load amber99SB & then gaff - if you do so and if the
geometry looks broken this is just another bug or an incompatibility
between the leaprc of amber99SB and gaff.
regards, Francois
Quoting Francesco Pietra <chiendarret.gmail.com>:
> Dear Francois:
> Attached the two full directories for PHA numbered 1 or 4. I did not
> attache the case of PHA #1 ending NH2 instead of NXT because the
> result was the same.
>
> Thanks a lot for your care. What I fear is some silly overlooking
> from my side.
>
> regards
> francesco
>
> On Wed, Oct 6, 2010 at 5:16 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>> Francesco,
>>
>> Could you send to my personal email address a tar.gz file
>> - with PHA numbered 4 with your LEaP script, frcmod, PDB file etc...
>> in one directory (your whole LEaP run 1)
>> - with PHA numbered 1 with your LEaP script, frcmod, PDB file etc...
>> in another directory (your whole LEaP run 2)
>>
>> I can try to have a look...
>>
>> regards, Francois
>>
>>
>> Quoting Francesco Pietra <chiendarret.gmail.com>:
>>
>>> It was a long story and surely tedious to follow by people uninvolved
>>> in attempts to generate this new residue in the Amber world. I repeat
>>> what I wrote. Leap crashed or, sometimes, hang up (on attempts to load
>>> the mol2 file) if PHA residue was numbered 4. If numbered 1, as in the
>>> files that I sent, leap produces prmtop/inpcrd. However, these files
>>> are not accepted by Chimera ("index out of range"), while VMD shows an
>>> extremely distorted molecule, especially as to the NH2 (of CONH2) and
>>> phenyl moieties.
>>>
>>> Susequently I also sent the frcmod file because, of course, it was
>>> loaded after the mol2 file in generating prmtop/frcmod.
>>>
>>> I also saved the *.lib file, if you want to see it.
>>>
>>> Leap comes from the same compilation, as antechamber, or ambertools
>>> 1.2, i.e., fully patched.
>>>
>>> I also wrote that it is the first time (out of very many) that I
>>> encounter such problems (distorted molecule on loading prmtop/inpcrd
>>> from antechamber-leap), from Amber 8 to my present version 10. I
>>> assumed that VMD is telling the truth.
>>>
>>> To chck if VMD is posing a false problem, I run antechamber-leap with
>>> sustiva.pdb (tutorial b4), encountering no problem. From prmto/inpcrd
>>> Chimera showed the arene bonds as pseudobonds, which must be a bug in
>>> Chimera as it occurs with all other my mol2 files for aromatic
>>> molecules, while VMD showed the molecule correctly. I checked the mol2
>>> format against its standard description without detecting anomalies
>>> but something wrong must have escaped my attention.
>>>
>>> thanks for your kind attention
>>> francesco
>>>
>>> On Wed, Oct 6, 2010 at 1:51 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>>>> Quoting Francesco Pietra <chiendarret.gmail.com>:
>>>>
>>>>> Sorry, forgot the addendum. Here attached. fc
>>>>
>>>> oh oh I forgot... When does LEaP crash ?
>>>>
>>>> I only tested loading only the mol2 file & it works.
>>>> I did not load any other file (before or after)...
>>>>
>>>> PHA = loadmol2 pha.NXT.mol2
>>>> => it works for me.
>>>>
>>>> regards, Francois
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Received on Thu Oct 07 2010 - 03:00:03 PDT
