The desktop motherboard died and parameterization data are there on the two
mirror raid HDs. Trying to recover data.
f
On Tue, Jan 6, 2015 at 7:01 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Francesco,
>
> > I forgot to ask why VMD does not show the existing (according to leap and
> > parmed.py) bonds between the protein backbone and the active center. In
> > contrast, all internal bonds in the active center are shown in VMD (they
> > where raised from a mol2 file with CONECT).
>
> vmd toto.mol2
> and
> vmd toto.parm7 toto.rst7
>
> should give you the same results if the mol2 file is used (LEaP) to
> generate the parm7/rst files
>
> on the contrary with
> vmd toto.pdb
> only bonds (based on vmd internal algo.) found by vmd will be created;
> i.e. only bonds below vmd internal thresholds will be found.
>
> we already discussed about that...
>
> regards, Francois
>
>
> > ---------- Forwarded message ----------
> > From: Francesco Pietra <chiendarret.gmail.com>
> > Date: Mon, Jan 5, 2015 at 9:37 AM
> > Subject: Re: [AMBER] Checking bonds commanded with leap
> > To: AMBER Mailing List <amber.ambermd.org>
> >
> >
> > 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
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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Received on Mon Jan 05 2015 - 23:30:03 PST
