VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Sep 14 2021 - 03:04:07 CDT

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
>>
>>
>>