From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Dec 29 2020 - 10:00:16 CST
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!uG9hsWDZaSG9-gnpoCQoKfYJXw3yH1_J6m_kesEMW600lkRTSdkfP8nmXs3oJxTsYA$
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!uG9hsWDZaSG9-gnpoCQoKfYJXw3yH1_J6m_kesEMW600lkRTSdkfP8nmXs1ovNZvDg$
>>
>>
>>
>> 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
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