VMD-L Mailing List

From: Raisa Carmen Andeme Ela (randemee_at_mtu.edu)
Date: Wed Apr 14 2021 - 19:31:56 CDT

Hello Josh,

Thank you so much for your assistance. After running it through
TKconsolo this is what the logfile says, and i still get the same image
type, please see below.: Running solvate with arguments: L57.psf L57.pdb -o
L57etoh -b 1.4 -minmax {{-40 -40 -40} {60 60 60}} -spsf etohbox.psf -spdb
etohbox.pdb -stop top_all36_cgenff.rtf -ws 82 -ks {name C1}
generating solute plus one replica of water...
generating water residue lists...
single water residue type, creating residue list...
replicating 8 water segments, 2 by 2 by 2
Solvate completed successfully.

On Wed, Apr 14, 2021 at 8:13 PM Vermaas, Josh <vermaasj_at_msu.edu> wrote:

> What is the output of the log? Everything looks plausible in the inputs
> (although isn’t the ethanol box 82x82x82?).
>
>
>
> What I would try is to do this once through the tkconsole and compare with
> the GUI output:
>
>
>
> package require solvate
>
> solvate input.psf input.pdb -o solvated -b 1.4 -minmax [list [list -40 -40
> -40] [list 60 60 60]] -spsf etohbox.psf -spdb etohbox.pdb -stop
> top_all36_cgenff.rtf -ws 82 -ks “name C1”
>
>
>
> This is what I used, so it should totally work.
>
>
>
> -Josh
>
>
>
> *From: *Raisa Carmen Andeme Ela <randemee_at_mtu.edu>
> *Date: *Wednesday, April 14, 2021 at 4:55 PM
> *To: *"vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>, "Vermaas, Josh" <
> vermaasj_at_msu.edu>
> *Subject: *VMD: ethanol solvation box
>
>
>
> Hello VMD Family,
>
>
>
> I have been trying to create a solvation box around a macromolecule
> (lignin); I am utilizing pre-equilibrated boxes created by Vermaas et al (
> 10.1021/acssuschemeng.0c07156
> <https://urldefense.com/v3/__http:/dx.doi.org/10.1021/acssuschemeng.0c07156__;!!HXCxUKc!lWQkTBLlZyHd1SwX6Q8WIiQqvQHK_6j1PxJDO4KE7W56QEtYvmt-r_DzbeHDPX0$>
> ).
>
>
>
> In VMD, I am inserting the following commands (please see image), but I am
> only getting carbon atoms making up the solvent box, and not full ethanol
> molecules (please see image attached); I have tried key selections "name
> C1, name O1, name HO1" and I still get this.
>
>
>
> Can anyone please assist me?
>
>
>
> Thank you so much in advance!
>
>
>
> Raisa
>
>
>


Captura_de_Pantalla_2021-04-14_a_la_s__20.29.50.png