VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Jul 07 2020 - 00:00:06 CDT

Hi Francesco,
Could you please post the first ~10 lines of your methanol pdb file, along
with the parameters used for solvate? Does your solvent PDB have segid QQQ
as noted in the solvate documentation?
Thanks,
Peter

On Mon, Jul 6, 2020 at 3:23 PM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> Because the full path is disliked, I tried again with the initial
> settings, except either "CB" or "MEOH" as key for the solvent box. In
> either case the error on the terminal was now explicit, albeit obscure to me
>
> psfgen) psf file does not contain cross-terms
>> psfgen) reading structure from psf file meoh.psf
>> psfgen) reading coordinates, insertion codes, and element symbols from
>> pdb file meoh.pdb
>> psfgen) atom mismatch in pdb file
>> psfgen) ATOM 1 CB MEOH 1 70.260 11.573 46.038 1.00
>> 0.00
>>
>
> which is the first line of the solvent box
>
> francesco
>
> ---------- Forwarded message ---------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Mon, Jul 6, 2020 at 6:44 PM
> Subject: vmd-l: Fwd: namd-l: Re: scripts to generate initial boxes of
> solvents
> To: <joshua.vermaas_at_gmail.com>, VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>
>
> Most unfortunately I was too quick: solvation occurred with TIP3.
>
> From the solvation plugin "A key selection which will occur once in each
> solvent residue (eg., "name OH2")" I used "MeOH" for methanol so that I
> have to search the solution elsewhere
>
> The solvation log reads:
>
>> Running solvate with arguments:
>> /home/francesco//meoenyne-O2_psfgen/meoenyne-O2.psf
>> /home/francesco/meoenyne-O2_psfgen/meoenyne-O2.pdb -o meoenyne-O2_pad3box
>> -s WT -x 3 -y 3 -z 3 +x 3 +y 3 +z 3 -b 2.4
>> generating solute plus one replica of water...
>> generating water residue lists...
>> single water residue type, creating residue list...
>> replicating 1 water segments, 1 by 1 by 1
>> Solvate completed successfully.
>>
>
> francesco
>
> ---------- Forwarded message ---------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Mon, Jul 6, 2020 at 5:25 PM
> Subject: Re: namd-l: Re: scripts to generate initial boxes of solvents
> To: Josh Vermaas <joshua.vermaas_at_gmail.com>
> Cc: NAMD <namd-l_at_ks.uiuc.edu>, James T. Metz <JamesTMetz_at_aol.com>
>
>
> I was just coming to amend. Assuming that the first line of the error log
> is what matters, by using the full path to meoh.pdb meoh.psf meoh.top,
> solvation runs OK
>
> again great advice from you. thanks
> francesco
>
> On Mon, Jul 6, 2020 at 5:18 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
> wrote:
>
>> 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
>>>>>
>>>>>