VMD-L Mailing List

From: Raisa Carmen Andeme Ela (randemee_at_mtu.edu)
Date: Thu Apr 15 2021 - 13:37:45 CDT

Thank you so very much, Josh! I truly appreciate it! I see, I’ll try implementing the same approach in the future.

Sincerely,
Raisa

Sent from my iPhone

> On Apr 15, 2021, at 11:40, Vermaas, Josh <vermaasj_at_msu.edu> wrote:
>
>  Hi Raisa,
>
> Some part of the solvent pdb didn't match the psf somehow, and so this was never running to completion. That is why I wanted the log. This is my modified script with the inputs you provided, and I've attached the output.
>
> package require solvate
> mol load psf etohbox.psf pdb etohbox.pdb
> animate write pdb newetohbox.pdb
> solvate L57.psf L57.pdb -o solvated -b 1.4 -minmax [list [list -40 -40 -40] [list 60 60 60]] -spsf etohbox.psf -spdb newetohbox.pdb -stop top_all36_cgenff.rtf -ws 82 -ks "name C1"
>
>
> -Josh
>
>> On 4/14/21 8:50 PM, Raisa Carmen Andeme Ela wrote:
>> Here they are:
>>
>> Thank you so much!
>>
>>
>>> On Wed, Apr 14, 2021 at 8:38 PM Vermaas, Josh <vermaasj_at_msu.edu> wrote:
>>> 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> 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).
>>>
>>>
>>>
>>> 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
>>>
>>>
>>>
>
> --
> Josh Vermaas
> Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology
> vermaasj_at_msu.edu
> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!t-M6yX-92A8NYsS-RRmDneVZkIXECebCwaQP_49WxdcWqUYwAPT38abeNo0gxrfWUA$
> <solvated.pdb>
> <solvated.psf>
> <test.tcl>