Re: Re: Re-center membrane protein

From: Ramon Mendoza Uriarte (ramendoza_at_uchicago.edu)
Date: Fri May 14 2021 - 12:51:41 CDT

For the future use the VMD mailing list for VMD related questions.

You can maybe try a different center first and then com:

pbc wrap -all -compound fragment -center origin
pbc wrap -all -compound fragment -center com -centersel "protein"
________________________________
From: Ropon-Palacios G. <biodano.geo_at_gmail.com>
Sent: Friday, May 14, 2021 10:21 AM
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>; Ramon Mendoza Uriarte <ramendoza_at_uchicago.edu>
Subject: Re: namd-l: Re: Re-center membrane protein

Iím using pbctools,

Following command : pbc wrap -compound fragment -center com -centersel "protein" -all -shiftcenter {0 1 0}

But bond of atoms crossing pbc box, how fix it bug?

From: <owner-namd-l_at_ks.uiuc.edu> on behalf of Ramon Mendoza Uriarte <ramendoza_at_uchicago.edu>
Reply-To: <namd-l_at_ks.uiuc.edu>, Ramon Mendoza Uriarte <ramendoza_at_uchicago.edu>
Date: Friday, May 14, 2021 at 12:19 PM
To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, "Ropon-Palacios G." <biodano.geo_at_gmail.com>
Subject: namd-l: Re: Re-center membrane protein

I would suggest looking at VMD's PBCTools Plugin:

http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/#:~:text=Since%20VMD%20version%201.8.6%2C%20the%20PBCTools%20plugin%20is,can%20be%20used%20within%20VMD%20without%20further%20preparation.s/pbctools/*:*:text=Since*20VMD*20version*201.8.6*2C*20the*20PBCTools*20plugin*20is,can*20be*20used*20within*20VMD*20without*20further*20preparation.__;I34lJSUlJSUlJSUlJSUlJSU!!BpyFHLRN4TMTrA!pV7zoCU5pUR4iqAHL3-T1Ogqk5IkRgtn7XSkacAayzACf9R4fDEKOmmQ-kmXqvYGhbPL$>

________________________________

From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Ropon-Palacios G. <biodano.geo_at_gmail.com>
Sent: Friday, May 14, 2021 10:02 AM
To: KS UIUC <namd-l_at_ks.uiuc.edu>
Subject: namd-l: Re-center membrane protein

Hello namd users,

I am running a simulation of a protein in membrane, which after 200 ns of simulation goes to a corner of the membrane and stays there for a long time, I want to perform the analyzes and I want to put it back in the center, how could I do this, without the links crossing the pbc box?.

Best,

Geo.

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