you can do this in many ways, here are two suggestions:
- if you load the prmtop into vmd prior to loading the coordinates, the
bonds in the prmtop, not the distance, will be used to determine which
bonds to show
- use parmed to write bond info with the printbonds command and a mask
restricting the list to SG atoms. See this example that shows the SG-SG
bond:
> printbonds .SG
Atom 1 Atom 2 R eq Frc Cnst
254 SG ( S) 658 SG ( S) 2.0380 166.0000
On Mon, Dec 14, 2020 at 8:27 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> Hello Bill
>
> Yes, I have unintentionally tried this before when including numerous
> peptides and not issuing the bond command for each separate peptide. Turns
> out that it worked fairly well for a single peptide, not so much when
> including multiple peptides and it pretty much resulted in the “analysis”
> suggested. The bond was not present, though neither was the CONECT info in
> the packmol output or the warning in leap.
>
> I was curious if it was possible to confirm a correct disulphide bond
> using parmed/cpptraj or some other tool available in the prmtop/inpcrd file
> before initiating the simulations. Checking in VMD or Chimera was my first
> instinct though turns out that GUI software can sometimes render sulphide
> bonds if the distance criteria seems reasonable, even if these are not
> present for the simulation engine.
>
> Best regards
> // Gustaf
>
>
> > On 14 Dec 2020, at 13:52, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> > If you run MD in vacuum at 100K or more, it should become apparent if
> > the bond is there.
> >
> > Bill
> >
> > On 12/14/20 12:54 AM, Gustaf Olsson wrote:
> >> Hello everyone
> >>
> >> I just want to double check something.
> >>
> >> I ran packmol including a peptide with a disulphide bond, using only
> the one peptide packmol seems to have added the correct conect record in
> the produced PDB file:
> >>
> >> CONECT 9 52
> >>
> >> Then when I run leap with 'bond sys.2.SG go.7.SG’ and try to write
> top/crd files leap exits with an error:
> >>
> >> !FATAL: Message: 1-4: cannot add bond 14 95
> >> This may be caused by duplicate bond specifications;
> >> for example, explicit bond commands in addition to PDB conect
> records.
> >>
> >> Is it safe to assume that the correct conect record in my PDB file is
> correctly applied in leap or is this something which should be “stripped”
> from the PDB and the bond created using leap.
> >>
> >> Best regards
> >> // Gustaf
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> >
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Received on Mon Dec 14 2020 - 06:30:07 PST
