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 - 08:30:08 PDT
