VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Wed Apr 14 2021 - 19:38:18 CDT

Can you attach your inputs? This is weird, since it totally has worked for me in the past.

-Josh

From: Raisa Carmen Andeme Ela <randemee_at_mtu.edu>
Date: Wednesday, April 14, 2021 at 8:32 PM
To: "Vermaas, Josh" <vermaasj_at_msu.edu>
Cc: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Re: ethanol solvation box

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<mailto: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<mailto:randemee_at_mtu.edu>>
Date: Wednesday, April 14, 2021 at 4:55 PM
To: "vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>" <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>, "Vermaas, Josh" <vermaasj_at_msu.edu<mailto: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