xparmed.py my.parm7
allowed to just clicking on "printBonds". As a mask, after some trial and
error, I used
":protein-residue","active-center-residue"
As far as I can understand, the output bond strength is the one I set in
the parameters, while Rmin does not correspond to the actual interatomic
distances (particularly as to the couple of too long bonds I have, 3 and
4A). Rather, it should correspond to just Rmin for such a bond. I was
surprised that it outputted Rmin for also iron-other_element bonds, most of
which are still to be assessed (I gave grossly estimated values, just to
see whether leap works with my files).
To the latter concern, has anyone developed and independent (independent
from tools on AmberTools) working out of the Cartesian matrix for complex
cases dealt with "ab initio" as in my case?
thanks
francesco
On Sun, Jan 4, 2015 at 5:35 PM, Gerald Monard <
Gerald.Monard.univ-lorraine.fr> wrote:
> Hello,
>
> Parmed (parmed.py) could help you with the "PrintBonds" command.
>
> Gerald.
>
> On 01/03/2015 07:25 PM, Francesco Pietra wrote:
> > Sorry for asking what will be common knowledge: where to check for bonds
> > formed that were commanded to leap (similarly to what is shown in psf
> > charmm files). I have both regular distances and too long distance for
> > regular bonds (between enzyme backbone and active center), none detected
> by
> > loading parm7/rst7 to vmd, while indicated on leap log.
> > thanks
> > francesco pietra
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
>
> ____________________________________________________________________________
>
> Prof. Gerald MONARD
> SRSMC, Université de Lorraine, CNRS
> Boulevard des Aiguillettes B.P. 70239
> F-54506 Vandoeuvre-les-Nancy, FRANCE
>
> e-mail : Gerald.Monard.univ-lorraine.fr
> tel. : +33 (0)383.684.381
> fax : +33 (0)383.684.371
> web : http://www.monard.info
>
>
> ____________________________________________________________________________
>
>
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Received on Mon Jan 05 2015 - 01:00:02 PST
