VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Sep 13 2021 - 12:00:20 CDT

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
>
>
>