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 - 07:00:04 PDT
