From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Dec 29 2020 - 10:00:16 CST
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.
----- 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?
> 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:
>> 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?
>>> 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
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:10 CST