VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Nov 20 2021 - 08:57:32 CST

Now, as a preamble to using the generated chloroform box, I have noticed
that autopsf/autopdb for the molecule to be solvated can be obtained from
the autopsf GUI by first deleting all topologies before adding those for
the intended molecule.

The same should be valid for the CHCL3box too, although I did not repeat
that autopsf from the GUI.

francesco

---------- Forwarded message ---------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Fri, Nov 19, 2021 at 10:15 PM
Subject: Re: vmd-l: Re: namd-l: namd minimization looking for wrong angle
To: Peter Freddolino <petefred_at_umich.edu>
Cc: <namd-l_at_ks.uiuc.edu> <namd-l_at_ks.uiuc.edu>, VMD Mailing List <
vmd-l_at_ks.uiuc.edu>

I thank you for your help. Your mode or running autopsf from the Tk console
worked also for me with vmd 1.9.4a55, and also for the box.

As usual with me, I run autopsf from the gui after having loaded the
solvent molecule (or solvent box). Then, in a sequence, Add the .rtf file,
Load input files, Guess and split chains, Create chains.

Thanks indeed

On Fri, Nov 19, 2021 at 6:03 PM Peter Freddolino <petefred_at_umich.edu> wrote:

> 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!qlH0tnidXr9S8Mzdd8L_u77JNtNMcBH00ZTSMv0BulcbtUqZWbHMvpBmBOaNaYuPvA$
>>>>> 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
>>>>>>>
>>>>>>