Re: Re: scripts to generate initial boxes of solvents

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Mon Jul 06 2020 - 10:18:03 CDT

Hi Francesco,

Tcl stack traces are always terrible, but I'd read the docs:
https://www.ks.uiuc.edu/Research/vmd/plugins/solvate/. The key selection is
meant to occur once per residue of the solvent. MeOH certainly doesn't
apply. I used "name CB", so that the carbon atom is used as the key
selection.

-Josh

On Mon, Jul 6, 2020, 9:01 AM Francesco Pietra <chiendarret_at_gmail.com> wrote:

> With methanol I got stuck at the solvate plugin and was unable to find a
> solution here at gihub.
>
> my settings:
> Box Padding 3
> Solvent Box PDB: meoh.pdb (the one you sent me)
> Solvent Box PSF: meoh.psf (the one you sent me)
> Solnet box topology: meoh.top (taken from CgenFF)
> Solvent box side length: 81 (measured from your psf/pdb)
> Solvent box key selection: MeOH
>
> From the below error log it is not clear to me what is wrong:
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> while executing
> "readpsf $solventpsf pdb $solventpdb"
> (procedure "solvate_core" line 224)
> invoked from within
> "solvate_core
> /home/francesco/work_raspaylines/meoenyne-O2_psfgen/meoenyne-O2.psf
> /home/francesco/work_raspaylines/meoenyne-O2_psfgen/meoenyne-O2.pdb -..."
> ("eval" body line 1)
> invoked from within
> "eval solvate_core $args "
> invoked from within
> "if $errflag { error $errMsg $savedInfo $savedCode }"
> (procedure "solvate" line 8)
> invoked from within
> "solvate
> {/home/francesco/work_raspaylines/meoenyne-O2_psfgen/meoenyne-O2.psf}
> {/home/francesco/work_raspaylines/meoenyne-O2_psfgen/meoenyne-O2.pdb} -o..."
> ("eval" body line 1)
> invoked from within
> "eval solvate $command_line"
> (procedure "::Solvate::run_solvate" line 96)
> invoked from within
> "::Solvate::run_solvate"
> invoked from within
> ".solvategui.solvate invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .solvategui.solvate"
> (command bound to event)
>
> Thanks for advice
> francesco
>
>
>
> On Sun, Jul 5, 2020 at 9:53 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
> wrote:
>
>> Hi Jim,
>>
>> If I do something, I do it for everyone, so I've now put the scripts on
>> github. https://github.com/jvermaas/solventboxgeneration This is what I
>> used for my own research to solvate lignin in all kinds of organic
>> solvents, so I do know that it works, but I haven't prettied up the scripts
>> very much to make the generally usable, so I welcome pull requests.
>>
>> -Josh
>>
>> On Sun, Jul 5, 2020 at 1:09 PM James T. Metz <jamestmetz_at_aol.com> wrote:
>>
>>> Joshua,
>>>
>>> Hello. I just noticed your post on the NAMD email list concerning
>>> scripts
>>> to generate initial boxes of solvents. I would be thankful if you would
>>> be
>>> willing to email me your script. Thank you.
>>>
>>> Regards,
>>> Jim Metz
>>>
>>>
>>> James T. Metz, Ph.D.
>>> President, Metz Research LLC
>>> 422 Cross Road
>>> Gurnee, IL 60031
>>> (847) 263 - 1514
>>> Please leave a message if you want a return call.
>>> JamesTMetz_at_AOL.com
>>> www.metzresearch.com
>>> www.linkedin.com/in/james-t-metz-phd-6117b3131
>>>
>>>

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