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 Wed Oct 06 2010 - 09:00:03 PDT
