Re: Re: scripts to generate initial boxes of solvents

From: Francesco Pietra (
Date: Mon Jul 06 2020 - 10:01:03 CDT

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: (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
/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
{/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
    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

On Sun, Jul 5, 2020 at 9:53 PM Josh Vermaas <>

> Hi Jim,
> If I do something, I do it for everyone, so I've now put the scripts on
> github. 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 <> 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.

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