Thank you Dan,
this is what I was looking for.
Thank you
Alessandro
Il 21/06/2016 16:16, Daniel Roe ha scritto:
> Hi,
>
> On Tue, Jun 21, 2016 at 3:27 AM, Alessandro Contini
> <alessandro.contini.unimi.it> wrote:
>> Since I've read in the
>> manual that distance based actions do not update on a per frame based, I
>> was trying both strip and mask commands but without success. Does
>> anybody can point me toward a way of doing this?
> Without knowing specifically what you tried, I can only offer general
> suggestions. The main issue with having a distance-based mask during
> trajectory processing is that the number of things selected will
> change, so things like writing to a trajectory format can become
> problematic. The way cpptraj currently does what you want is via the
> 'mask' command, which allows you to output a PDB or Mol2 file for each
> frame based on whatever mask you give it. For example, to select all
> water residues (named WAT) within 3.0 Angstroms of residue 5 and write
> them to Mol2 files:
>
> mask (:5<:3.0)&:WAT maskmol2 mask.mol2
>
> Hope this helps,
>
> -Dan
>
>> Thank you and best regards
>>
>> Alessandro
>>
>> --
>> Alessandro Contini, PhD
>> Dipartimento di Scienze Farmaceutiche
>> Sezione di Chimica Generale e Organica "A. Marchesini"
>> Via Venezian, 21 20133 Milano
>> tel. +390250314480
>> e-mail alessandro.contini.unimi.it
>> skype alessandrocontini
>>
>> http://www.scopus.com/authid/detail.url?authorId=7003441091
>> http://orcid.org/0000-0002-4394-8956
>> http://www.researcherid.com/rid/F-5064-2012
>>
>>
>>
>>
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>
>
--
Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
e-mail alessandro.contini.unimi.it
skype alessandrocontini
http://www.scopus.com/authid/detail.url?authorId=7003441091
http://orcid.org/0000-0002-4394-8956
http://www.researcherid.com/rid/F-5064-2012
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Received on Wed Jun 22 2016 - 03:30:03 PDT
