VMD-L Mailing List
From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Sep 13 2021 - 12:45:15 CDT
- Next message: Runak R: "Question about secondary structure analysis"
- Previous message: Peter Freddolino: "Re: Fwd: autopsf with many modifiers"
- In reply to: Peter Freddolino: "Re: Fwd: autopsf with many modifiers"
- Next in thread: Francesco Pietra: "Fwd: Fwd: autopsf with many modifiers"
- Reply: Francesco Pietra: "Fwd: Fwd: autopsf with many modifiers"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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
>>
>>
>>
- Next message: Runak R: "Question about secondary structure analysis"
- Previous message: Peter Freddolino: "Re: Fwd: autopsf with many modifiers"
- In reply to: Peter Freddolino: "Re: Fwd: autopsf with many modifiers"
- Next in thread: Francesco Pietra: "Fwd: Fwd: autopsf with many modifiers"
- Reply: Francesco Pietra: "Fwd: Fwd: autopsf with many modifiers"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]