VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Fri Nov 19 2021 - 11:02:59 CST

How were you running autopsf, and with what version of vmd?

autopsf -mol 0 -top 1009279.rtf
(after having loaded chcl3.pdb) works fine for me with the files that you
provided, using vmd1.9.4a51

Best,
Peter

On Fri, Nov 19, 2021 at 11:56 AM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> 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!vfnALz6qcNLckwdkOL60Aa54eZb1UXLBAyVBK8n4_Wrb8wbvq_unXusdqGrHc4nUrA$
>>>> 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
>>>>>>
>>>>>