From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Nov 19 2021 - 10:55:59 CST
Unfortunately I have no access to that journal. At any event, I never use
SHAKE, so that I parameterized CHCL3 on the MATCH server, getting the
attached rtf. On that basis, I first tried to generate psf/pdb for a single
CHCL3 molecule. With autopsf the error.log was
ERROR: failed on end of segment
> 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 $segid {
> pdb $segfile
>
# We alias the C-terminal OXT atoms to OT2 so that psfgen has to
> guess one atom less.
> # Otherwise psf..."
> (procedure "psfsegments" line 37)
> invoked from within
> "psfsegments $logfileout"
> (procedure "::autopsf::afterchains_gui" line 66)
> invoked from within
> "::autopsf::afterchains_gui"
> invoked from within
> ".autopsf.chains.finish invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .autopsf.chains.finish"
> (command bound to event)
while the terminal last lines told
segfiles CHCl3_autopsf-temp.pdb_XO1.pdb
> CHCl3_autopsf-temp.pdb_XO1.pdb
> 1 4
> psfgen) building segment XO1
> psfgen) reading residues from pdb file CHCl3_autopsf-temp.pdb_XO1.pdb
> psfgen) unknown residue type CCL3
> psfgen) extracted 1 residues from pdb file
> psfgen) setting patch for first residue to none
> psfgen) setting patch for last residue to none
> Info: generating structure...
> psfgen) unknown residue type CCL3
>
Then, I made recourse to vmd text mode, getting attached chcl3.psf/pdb
without any issue.
However, I needed psf/pdb for the solvent box, again from the box generated
with packmol that I reported previously. In this case I was not aware of
any trick to avoid writing 1000-fold inputs on the .gen file, so that I
tried with autopsf. The last lines on the terminal were:
psfgen) extracted 1000 residues from pdb file
> psfgen) setting patch for first residue to none
> psfgen) setting patch for last residue to none
> Info: generating structure...
> psfgen) unknown residue type CCL3
> Segmentation fault
>
Obviously CCL3 was and is the residue. Probably, without additional
information no one will be able to suggest a remedy for autopsf (perhaps,
however, suggesting how to deal with vmd text mode for the solvent box,
i.e. a shortcut for the onethousand blocks)
Thanks for your attention
francesco
On Fri, Nov 19, 2021 at 2:57 PM Peter Freddolino <petefred_at_umich.edu> wrote:
> Based on the comments in that topology file (which I had to google -- it
> would really help to include such things in the mailing list discussion),
> it looks like those CL-CL and other problematic bonds are present only for
> SHAKE. That suggests to me that this is supposed to be a rigid chloroform
> model, which might not be possible in NAMD. Did you check the original
> paper (W. Dietz, K. Heinzinger, Ber. Bunsen-Ges. Phys. Chem 1985, 89, 968)
> for how this is supposed to be implemented?
> Thanks,
> Peter
>
> On Fri, Nov 19, 2021 at 4:33 AM Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> Hi Peter
>> Bonds between all couple of atoms, even CL-CL
>>
>>> 5000 !NBOND: bonds
>>> 1 2 1 4 1 5 1
>>> 6
>>> 2 3 7 8 7 10 7
>>> 11
>>> 7 12 8 9 13 14 13
>>> 16
>>> 13 17 13 18 14 15 19
>>> 20
>>> 19 22 19 23 19 24 20
>>> 21
>>>
>> where atom numbering is
>>
>>> 5000 !NATOM
>>> 1 AO1 1 CCL3 C CCM 0.179000 12.0110 0
>>> 2 AO1 1 CCL3 CL1 CLCM -0.087000 35.4500 0
>>> 3 AO1 1 CCL3 CL2 CLCM -0.087000 35.4500 0
>>> 4 AO1 1 CCL3 CL3 CLCM -0.087000 35.4500 0
>>> 5 AO1 1 CCL3 HX HCM 0.082000 1.0080 0
>>>
>>
>>> All such bonding is also evident from loading psf/pdb to vmd.
>>>
>>> I started from a box prepared with packmol, and I tried also adding TER
>>> between residues
>>> HEADER
>>> TITLE Built with Packmol
>>> REMARK Packmol generated pdb file
>>> REMARK Home-Page: https://urldefense.com/v3/__http://m3g.iqm.unicamp.br/packmol__;!!DZ3fjg!s6lbYqArpiNe-Obx81ImBSD98ZIZEvVBLc8BZnnzXEAVk3UpETJeC8YQpDdQSBNkdg$
>>> REMARK
>>> HETATM 1 CL1 CCL3A 1 30.522 5.429 3.173 1.00 0.00
>>> CL
>>> HETATM 2 CL2 CCL3A 1 30.670 3.053 4.852 1.00 0.00
>>> CL
>>> HETATM 3 CL3 CCL3A 1 31.018 2.823 1.969 1.00 0.00
>>> CL
>>> HETATM 4 C CCL3A 1 31.285 3.845 3.391 1.00 0.00
>>> C
>>> HETATM 5 HX CCL3A 1 32.361 3.996 3.509 1.00 0.00
>>> H
>>> TER
>>> HETATM 6 CL1 CCL3A 2 3.817 17.228 1.210 1.00 0.00
>>> CL
>>> HETATM 7 CL2 CCL3A 2 1.496 17.919 2.829 1.00 0.00
>>> CL
>>> HETATM 8 CL3 CCL3A 2 3.573 16.195 3.922 1.00 0.00
>>> CL
>>> HETATM 9 C CCL3A 2 3.231 17.561 2.849 1.00 0.00
>>> C
>>> HETATM 10 HX CCL3A 2 3.759 18.439 3.230 1.00 0.00
>>> H
>>> TER
>>>
>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>> No such problems encountered in making a MEOH box, starting from "RESI
>> MEOH" in CGenFF. Clear, not interacting MEOH molecules where obtained,
>> with psf indicating only the correct bonds.
>>
>> With CHARMM36/CGenFF the only source of topology for CHCL3 is
>> toppar_chloroform_dh.str
>> I can't understand where I am wrong with CHCL3
>> Thanks for advice
>> francesco
>>
>> On Thu, Nov 18, 2021 at 3:38 PM Peter Freddolino <petefred_at_umich.edu>
>> wrote:
>>
>>> Have you looked at the bonds in your psf to make sure they are correct?
>>> This looks like you've hydrogen atoms that have two bonds...
>>> Best,
>>> Peter
>>>
>>> On Thu, Nov 18, 2021 at 5:42 AM Francesco Pietra <chiendarret_at_gmail.com>
>>> wrote:
>>>
>>>> It seems thatb the str used is inadequate. Alsdo adjusting angles in
>>>> str, namd assks for dihedrals
>>>> fp
>>>>
>>>> On Thu, Nov 18, 2021 at 9:29 AM Francesco Pietra <chiendarret_at_gmail.com>
>>>> wrote:
>>>>
>>>>> While attempting to minimize a CHCL3 box built from CHARMM36-provided
>>>>> toppar_chloroform_dh.str, namd crashes
>>>>>
>>>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS 1
>>>>>> 5 4)
>>>>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CCM HCM CLCM (ATOMS
>>>>>> 1 5 4)
>>>>>>
>>>>>
>>>>> Actually, the prm part of the str (which was read by namd) l correctly
>>>>> furnishes
>>>>>
>>>>>> ANGLES
>>>>>> CLCM CCM CLCM 0.0 111.30
>>>>>> HCM CCM CLCM 0.0 107.57
>>>>>>
>>>>>
>>>>> Why is namd looking for those wrong angles? The central atom is carbon
>>>>> not hydrogen.
>>>>>
>>>>> Thanks for advice
>>>>> francesco pietra
>>>>>
>>>>
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