We don't have enough information. Whne you say your molecule is broken,
exactly which bond is missing, and how does that compare to the list of
bonds you wrote in your input?
On Fri, Jan 17, 2020, 10:16 AM MYRIAN TORRES RICO <myriam.torres.iiq.csic.es>
wrote:
> Hi,
>
> I have checked the previous step in the molecular dynamics, and tleap
> is the problem. This program generate three files: file.top,
> file_leap.pdb and file.crd.
> When I load .top and .crd in the VMD, the structure of my molecule
> appears broken...and I have compared with other cases and the molecule
> is fine.
> Any idea?
>
> This is my script in case it helps you:
>
>
> source leaprc.Alba
> ##############################
> # INFO
> ##############################
> # Wrap total de l'ultim pdb
> # i treure topologia per:
> # "inconsistent amber top and
> # coord file" en ambertogromos
> ##############################
>
> #galc=loadpdb ja.pdb
> galc=loadpdb mdk2rig.pdb
>
> ############BONDS#############
> # S-S bonds
> bond galc.18.SG galc.42.SG
> bond galc.26.SG galc.51.SG
> bond galc.33.SG galc.55.SG
> bond galc.65.SG galc.97.SG
> bond galc.75.SG galc.107.SG
>
> # Sugar-GLU bond
> bond galc.138.C1 galc.137.O1
> bond galc.139.C1 galc.138.O3
> bond galc.140.C1 galc.139.O4
> bond galc.141.C1 galc.140.O3
> bond galc.142.C1 galc.141.O4
> bond galc.143.S1 galc.138.O6
> bond galc.144.S1 galc.138.O4
> bond galc.145.S1 galc.140.O6
> bond galc.146.S1 galc.140.O4
> bond galc.147.S1 galc.142.O6
> bond galc.148.S1 galc.142.O4
> # Delete unusual bond
> #deletebond galc.472.C galc.473.C1
> #############################
>
> # Check and desc
> check galc
> desc galc
>
> # Add ions, solvate and set the box
> addions2 galc Cl- 4
> solvatebox galc TIP3PBOX 15.0
> setbox galc vdw
> # Save top, crd and pdb
> saveamberparm galc smp-199-mdk2rig.top smp-199-mdk2rig.crd
> savepdb galc smp-199-mdk2rig_leap.pdb
>
> quit
>
>
>
> S-S bonds: This part belong to protein, I check the aa which have S-S bond
>
> Sugar-GLU bond: My pentasaccharide, I describe the conexion between
> the residues.
>
>
>
> Thanx in advance
>
>
> Myriam
>
> Carlos Simmerling <carlos.simmerling.gmail.com> escribió:
>
> > No we were talking about the parmed program included in AmberTools.
> >
> > Do not do any processing before viewing the structure. Load into VMD the
> > prmtop used for the minimization or md, and then load into that molecule
> > the restart file using amber7 restart format in VMD. This will eliminate
> > possible problems in your fixatomorder command (I do not know what this
> is
> > doing).
> >
> >
> > On Wed, Jan 15, 2020, 8:52 AM MYRIAN TORRES RICO <
> myriam.torres.iiq.csic.es>
> > wrote:
> >
> >> Ok, I think that I use parm...Can be this? Do you refer to this?:
> >>
> >>
> >> parm smp-199-mdk0rig.top
> >> trajin smp-199mdk0rig_vcon3.mdcrd
> >> fixatomorder outprefix reorder
> >> trajout reorder-smp-199mdk0_vcon3.nc
> >>
> >> I use this script to see the final structure by VMD
> >>
> >>
> >> Thanx in advance,
> >>
> >>
> >> Myriam
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> Carlos Simmerling <carlos.simmerling.gmail.com> escribió:
> >>
> >> > The follow Dave's advi e and use parmed. Printbonds should be what you
> >> > want.
> >> > https://parmed.github.io/ParmEd/html/parmed.html
> >> >
> >> >
> >> > On Wed, Jan 15, 2020, 6:44 AM MYRIAN TORRES RICO <
> >> myriam.torres.iiq.csic.es>
> >> > wrote:
> >> >
> >> >> Yes, I use coordinates (.mdcrd or .crd) and prmtop in the VMD. I have
> >> >> attach a photo with the result of my tetrasaccharide.
> >> >> it's the first time that happens to me...
> >> >>
> >> >> Myriam
> >> >>
> >> >> Carlos Simmerling <carlos.simmerling.gmail.com> escribió:
> >> >>
> >> >> > Just one quick thing to check - how are you visualizing the ligand?
> >> Are
> >> >> you
> >> >> > using coordinates and prmtop (such as in Vmd) or are you allowing
> the
> >> viz
> >> >> > software to determine bonds? The latter might not reliably
> represent
> >> the
> >> >> > bonds used in md. How far apart do the ligand pieces move?
> >> >> >
> >> >> >
> >> >> > On Wed, Jan 15, 2020, 6:26 AM MYRIAN TORRES RICO <
> >> >> myriam.torres.iiq.csic.es>
> >> >> > wrote:
> >> >> >
> >> >> >> I have visualized the structure in the heat step, and my molecule
> is
> >> >> >> broken, so in effect, the problem is in minimization step. But,
> this
> >> >> >> phase doesn't create min.mdcrd file...
> >> >> >>
> >> >> >> "use parmed to check the prmtop file for the presence/absence of
> >> bonds
> >> >> >> between the parts of the ligand that are no longer together"
> >> >> >>
> >> >> >> How I do this?
> >> >> >>
> >> >> >> Thanx in advance
> >> >> >>
> >> >> >>
> >> >> >> Myriam
> >> >> >>
> >> >> >> David Case <david.case.rutgers.edu> escribió:
> >> >> >>
> >> >> >> > On Tue, Jan 14, 2020, MYRIAN TORRES RICO wrote:
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> I'm looking for any idea about a problem with my results. I
> have
> >> >> >> >> launched a molecular dynamic of my complex ligand-protein (my
> >> ligand
> >> >> >> >> is a tetrasaccharide), and when finished all steps
> (minimization,
> >> >> >> >> heat, pressure and volume), my molecule is split.
> >> >> >> >
> >> >> >> > I'm guessing this means that some bond is missing in the
> >> carbohydrate
> >> >> >> > part. You'll probably see what is happening even after the
> >> >> minimization
> >> >> >> > step. Visualize the minimized structure and see which bonds are
> >> >> >> > "broken"; use parmed to check the prmtop file for the
> >> presence/absence
> >> >> >> > of bonds between the parts of the ligand that are no longer
> >> >> "together".
> >> >> >> >
> >> >> >> > Then, you will need to figure out what went wrong. It's a good
> >> idea
> >> >> to
> >> >> >> > set up just the ligand, and run a minimization on it. That
> gives
> >> you
> >> >> a
> >> >> >> > lot fewer things to look at.
> >> >> >> >
> >> >> >> > ....dac
> >> >> >> >
> >> >> >> >
> >> >> >> > _______________________________________________
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> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
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> >> >>
> >> >>
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> >>
> >>
> >>
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Received on Fri Jan 17 2020 - 07:30:02 PST
