AMBER Archive (2007)

Subject: Re: AMBER: Fwd: antechamber save prmtop inpcrd

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Jul 04 2007 - 11:54:08 CDT

No warning about lacking parameters had appeared, either with my molecule or
sustiva after that the frcmod file had been loaded.

I believe I have added to my original email that I later checked the issue with
antechamber-sustiva tutorial. The outcome was the same as with my molecule
(prmtop and inpcrd files were correct for sustiva; not yet used for my
molecule)..

In both cases (sustiva and my own molecule) the saveparm ... command reported
on the xleap screen (last visible portion for ) the same substance. For my
molecule:

........
<EQA 1> : C39 C41 C40 H43
<EQA 1> : C40 C38 C39 O10

total 30 improper torsions applied

28 improper torsions in old prep form

Building H-Bond parameters.

Not masking per-residue atom chain types.

Marking per-residue atom chain types.
(Residues lacking connect 0/connect 1-
these don't have chain type marked:

res total affected

WAT 1667
)

(no restraints)

I am not implying that there can not be problems. When I first carried out the
antech-sustiva tutorial, I quitted from xleap by killing the X system
(Ctrl-Alt-Backspace) so that I could not notice what I later noticed with my
molecule by quitting xlead from its menu commands.

Thanks

francesco pietra

--- "David A. Case" <case_at_scripps.edu> wrote:

> On Tue, Jul 03, 2007, Francesco Pietra wrote:
>
> > Warning "not saved" on quitting xleap after having run
> >
> > saveamberparm ...
> >
> > is typical behavior of xleap
>
> I don't think this is correct. If the actual statement is "Parameter file
> was
> not saved", that means just what it says. There should always be error
> messages preceeding this that indicate the problem (usually missing
> parameters).
>
> You might want to compare your results with the leap.out.save script
> in $AMBERHOME/test/antechamber/sustiva, for example.
>
> ...dac
>
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