From: Peter Freddolino (petefred_at_umich.edu)
Date: Sun Sep 19 2021 - 00:11:26 CDT

Hi Francesco,
Thanks for the update. Glad to hear it. (and sorry for the slow reply - got
caught up in a bunch of other items this week)
Best,
Peter

On Tue, Sep 14, 2021 at 5:30 AM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> Hi Peter
> all patches did perfectly their job for the 18-chains ensemble. Solvation
> and neutralization, or neutralization + 0.15M NaCl, also OK.
>
> Thanks and my apologies for untimely post
>
> francesco
>
> ---------- Forwarded message ---------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Tue, Sep 14, 2021 at 10:04 AM
> Subject: Fwd: vmd-l: Fwd: autopsf with many modifiers
> To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>, <petefred_at_umich.edu>
>
>
> Hi peter
> A quick note to avoid wasting time from you and other: my silly mistake
> was to add patches and generating psf/pdb before having generated psf/pdb
> without added patches
>
> In this case I also used the charmm36
> toppar_c36_2016_mass_orig/stream/prot/toppar_all36_prot_arg0.str:PRES RN2
> instead of the charmm27 RN2 patch.
>
> Thus, by first generating psf/pdb in the AutoPSF gui without patches, then
> adding patches and re-generating psf/pdb again (which is clearly indicated
> along the gui), psf/pdb were obtained for the 18-chains ensemble. I still
> have to examine the generated files accurately, because the LSN patch for
> neutral LYS worked perfectly, while ASPP for neutral ASP did not work
> (protonated ASP was obtained, perhaps because of another silly mistake).
> All patches were now from charmm36.
>
> thanks
> francesco
>
>
>
> ---------- Forwarded message ---------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Mon, Sep 13, 2021 at 7:45 PM
> Subject: Re: vmd-l: Fwd: autopsf with many modifiers
> To: Peter Freddolino <petefred_at_umich.edu>
> Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>
>
> Hi Peter
> I was using AutoPSF with vmd 1.9.3 on Linux.
> Added all charmm36 files topology files as indicated in my previous mail
> Then, "Create chains worked perfectly
> Then, I added patches, one by one, using the "Add patch" of AutoPSF,
> filling
>
> Patch type ...Segment 1....Residue 1
>
> Finally "Apply patches and finish PSF/PDB
>
>
> raising the error that I reported
>
> I hope to have answered correctly
>
> francesco
>
>
>
> On Mon, Sep 13, 2021 at 7:00 PM Peter Freddolino <petefred_at_umich.edu>
> wrote:
>
>> Hi Francesco,
>> If I am understanding the question properly, the syntax that you'll want
>> to follow is:
>>
>> -patch { {PATCH1 CHAIN1 RES1} {PATCH2 CHAIN2 RES2} ... } etc
>>
>> For example, if I wanted to make two disulfide bonds from residue 139-151
>> and 152-193 in chain A of the input file, I would do
>>
>> -patch { {DISU A 139 A 151} {DISU A 152 A 193} }
>>
>> If this is not what you are after, could you please give an example of
>> the command line that you're trying?
>>
>> Best,
>> Peter
>>
>> On Mon, Sep 13, 2021 at 11:20 AM Francesco Pietra <chiendarret_at_gmail.com>
>> wrote:
>>
>>> As a further information, besides top_all36_cgenff.rtf (for thge
>>> ligand), top_all36_lipid.rtf, top_all_36_na.rtf, top_all36_na.rtf,
>>> toppar_water_ions.str also
>>> CHARMM_FF/charmm27_36_for_NAMD/toppar_c36_Aug15/stream/prot/toppar_all36_prot_arg0.str
>>> was uploaded for non protonated ARG
>>> fp
>>>
>>> ---------- Forwarded message ---------
>>> From: Francesco Pietra <chiendarret_at_gmail.com>
>>> Date: Mon, Sep 13, 2021 at 11:58 AM
>>> Subject: Fwd: autopsf with many modifiers
>>> To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>>>
>>>
>>> Sorry for this untimely and naive post.
>>>
>>> Actually, autopsf gen without patches was successful and I noticed that
>>> HIS was assigned as HSD by default, which is acceptable for non protonated
>>> HIS. Also. ILE CD1 -> CD by default.
>>>
>>> On applying HS2 ASPP RN2 and LSN patches, Error: could not open "": no
>>> such file or directory. The log file reads:
>>> couldn't open "": no such file or directory
>>> couldn't open "": no such file or directory
>>> while executing
>>> "open $logfilename a"
>>> (procedure "::autopsf::makepatches_gui" line 13)
>>> invoked from within
>>> "::autopsf::makepatches_gui"
>>> invoked from within
>>> ".autopsf.patches.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.patches.finish"
>>> (command bound to event)
>>>
>>> I can't understand, not seeing any "" file anywhere.
>>> Thanks for advice
>>> francesco pietra
>>>
>>>
>>> ---------- Forwarded message ---------
>>> From: Francesco Pietra <chiendarret_at_gmail.com>
>>> Date: Sat, Sep 11, 2021 at 4:21 PM
>>> Subject: autopsf with many modifiers
>>> To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>>>
>>>
>>> With protein-nucleic systems composed of a large number of subunits, the
>>> use of autopsf avoids the burden required by the preparation of psfgen.
>>> However, going on by trial and error (which is my case), resetting any time
>>> all modifiers becomes more than annoying.
>>>
>>> To this regard, should the same patch for different residues be
>>> specified line-by-line
>>> patch HS2 HIS:11H
>>> patch HS2 HIS:243J
>>> patch HS2 HIS:256J
>>> patch HS2 HIS:259J
>>> or can be combined in a single line?
>>>
>>> Moreover, how to specify pdbalias (and, like above, could these be
>>> combined in a single line for the same alias?):
>>> pdbalias atom ILE CD1 CD
>>> pdbalias residue HIS:209F HSE
>>> pdbalias residue HIS:216G HSE
>>> pdbalias residue HIS:218G HSE
>>> pdbalias residue HIS:231J HSE
>>> pdbalias residue HIS:133N HSE
>>> pdbalias residue HIS:25P HSE
>>> pdbalias residue HIS:28P HSE
>>> pdbalias residue HIS:7Q HSE
>>>
>>> regenerate angles dihedrals
>>> guesscoord
>>>
>>> Thanks a lot for advice
>>> francesco pietra
>>>
>>>
>>>