Re: path CV

From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Thu Jan 28 2021 - 02:11:13 CST

Hi Jerome,
thanks

Stefano

Il giorno mar 29 dic 2020 alle ore 17:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>
ha scritto:

> Hi Stefano,
>
> Yes, you can also specify a PDB file with any number of atoms to provide
> coordinates. What matters is that exactly the right number of atoms are
> flagged on the O or B column.
>
> https://urldefense.com/v3/__http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html*sec:colvars_pdb_format__;Iw!!DZ3fjg!v3UZvjyBp2WFSep_TKM9QCpbsLuKRN54w-VYHdj0Ts5iS0GswB5SJifx9LalNIm0QQ$
>
> Jerome
>
> ----- On 18 Déc 20, at 18:22, Stefano Guglielmo stefano.guglielmo_at_unito.it
> wrote:
>
> > Hello Giacomo,
> > thanks for your reply.
> > Would it work if I include the pdb files of the whole protein (without
> > solvent and so on) and then specify atoms with atomNumbers for
> calculating
> > the path? and eventually can I specify fittingAtoms the same way, i.e.
> > using atomNumbers referring to the refPositionsFileN files?
> >
> > Thanks
> >
> > Il giorno ven 18 dic 2020 alle ore 17:36 Giacomo Fiorin <
> > giacomo.fiorin_at_gmail.com> ha scritto:
> >
> >> Hello Stefano, yes. The simplest would be to just include in each file
> >> only coordinates for the atoms that were selected, in the same order as
> the
> >> selection. For precision, XYZ files are recommended:
> >>
> >>
> https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html*sec:colvars_xyz_format__;Iw!!DZ3fjg!v3UZvjyBp2WFSep_TKM9QCpbsLuKRN54w-VYHdj0Ts5iS0GswB5SJifx9Lbb7BOvcQ$
> >>
> >>
> >>
> >> On Fri, Dec 18, 2020 at 9:50 AM Stefano Guglielmo <
> >> stefano.guglielmo_at_unito.it> wrote:
> >>
> >>> Dear all,
> >>> is it possible to use as refPositionsFileN N files containing only a
> part
> >>> of the system, let's say the protein without water and ions?
> >>>
> >>> Thanks
> >>> Stefano
> >>>
> >>> --
> >>> Stefano GUGLIELMO PhD
> >>> Associate Professor of Medicinal Chemistry
> >>> Department of Drug Science and Technology
> >>> Via P. Giuria 9
> >>> 10125 Turin, ITALY
> >>> ph. +39 (0)11 6707178
> >>>
> >>>
> >
> > --
> > Stefano GUGLIELMO PhD
> > Associate Professor of Medicinal Chemistry
> > Department of Drug Science and Technology
> > Via P. Giuria 9
> > 10125 Turin, ITALY
> > ph. +39 (0)11 6707178
>

-- 
Stefano GUGLIELMO PhD
Associate Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178

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