VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Jul 07 2020 - 01:58:10 CDT

By adding segid to the pdb file (letting psf as it was) and using the
parameters as before

CRYST1 80.000 80.000 80.000 90.00 90.00 90.00 P 1 1
ATOM 1 CB MEOHX 1 70.260 11.573 46.038 1.00 0.00 QQQ

ATOM 2 OG MEOHX 1 69.560 11.840 47.252 1.00 0.00 QQQ

ATOM 3 HG1 MEOHX 1 70.191 12.189 47.890 1.00 0.00 QQQ

ATOM 4 HB1 MEOHX 1 69.551 11.168 45.283 1.00 0.00 QQQ

ATOM 5 HB2 MEOHX 1 71.062 10.822 46.209 1.00 0.00 QQQ

ATOM 6 HB3 MEOHX 1 70.710 12.507 45.636 1.00 0.00 QQQ

ATOM 7 CB MEOHX 2 42.919 1.040 78.112 1.00 0.00 QQQ

ATOM 8 OG MEOHX 2 42.788 1.172 76.698 1.00 0.00 QQQ

ATOM 9 HG1 MEOHX 2 42.162 1.882 76.520 1.00 0.00 QQQ

ATOM 10 HB1 MEOHX 2 43.638 0.224 78.344 1.00 0.00 QQQ

ATOM 11 HB2 MEOHX 2 41.938 0.788 78.571 1.00 0.00 QQQ

ATOM 12 HB3 MEOHX 2 43.300 1.985 78.557 1.00 0.00 QQQ

ATOM 13 CB MEOHX 3 31.982 71.723 3.797 1.00 0.00 QQQ

the solvate.log was
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
    while executing
"segment ${prefix}$nstr {
          first NONE
          last NONE
          foreach res $wat_unique_res resname $wat_unique_resname {
            resi..."
    (procedure "solvate_core" line 404)
    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)

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Tue, Jul 7, 2020 at 8:01 AM
Subject: Re: vmd-l: Fwd: namd-l: Re: scripts to generate initial boxes of
solvents
To: Peter Freddolino <petefred_at_umich.edu>
Cc: Josh Vermaas <joshua.vermaas_at_gmail.com>, VMD Mailing List <
vmd-l_at_ks.uiuc.edu>

Hi Peter

meoh.pdb
CRYST1 80.000 80.000 80.000 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 CB MEOH 1 70.260 11.573 46.038 1.00 0.00

ATOM 2 OG MEOH 1 69.560 11.840 47.252 1.00 0.00

ATOM 3 HG1 MEOH 1 70.191 12.189 47.890 1.00 0.00

ATOM 4 HB1 MEOH 1 69.551 11.168 45.283 1.00 0.00

ATOM 5 HB2 MEOH 1 71.062 10.822 46.209 1.00 0.00

ATOM 6 HB3 MEOH 1 70.710 12.507 45.636 1.00 0.00

ATOM 7 CB MEOH 2 42.919 1.040 78.112 1.00 0.00

ATOM 8 OG MEOH 2 42.788 1.172 76.698 1.00 0.00

ATOM 9 HG1 MEOH 2 42.162 1.882 76.520 1.00 0.00

ATOM 10 HB1 MEOH 2 43.638 0.224 78.344 1.00 0.00

ATOM 11 HB2 MEOH 2 41.938 0.788 78.571 1.00 0.00

ATOM 12 HB3 MEOH 2 43.300 1.985 78.557 1.00 0.00

ATOM 13 CB MEOH 3 31.982 71.723 3.797 1.00 0.00

meoh.psf
 REMARKS original generated structure x-plor psf file
 REMARKS topology /home/josh/toppar/top_all36_cgenff.rtf
 REMARKS segment QQQ { first NONE; last NONE; auto angles dihedrals }

    6000 !NATOM
         1 QQQ 0 MEOH CB CG331 -0.040000
12.0110 0
         2 QQQ 0 MEOH OG OG311 -0.650000
15.9994 0
         3 QQQ 0 MEOH HG1 HGP1 0.420000
 1.0080 0
         4 QQQ 0 MEOH HB1 HGA3 0.090000
 1.0080 0
         5 QQQ 0 MEOH HB2 HGA3 0.090000
 1.0080 0
         6 QQQ 0 MEOH HB3 HGA3 0.090000
 1.0080 0
         7 QQQ 1 MEOH CB CG331 -0.040000
12.0110 0
         8 QQQ 1 MEOH OG OG311 -0.650000
15.9994 0
         9 QQQ 1 MEOH HG1 HGP1 0.420000
 1.0080 0
        10 QQQ 1 MEOH HB1 HGA3 0.090000
 1.0080 0
        11 QQQ 1 MEOH HB2 HGA3 0.090000
 1.0080 0
        12 QQQ 1 MEOH HB3 HGA3 0.090000
 1.0080 0
        13 QQQ 2 MEOH CB CG331 -0.040000
12.0110 0

Box Size: use molecular dimensions
Box Padding: 3
Solvent BOX PDB: meoh.pdb
Solvent BOX PSF: meoh.psf
Solven box side length: 81
Solvent Box key select ion: either CB or MEOH

On Tue, Jul 7, 2020 at 7:00 AM Peter Freddolino <petefred_at_umich.edu> wrote:

> 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
>>>>>>
>>>>>>