I just solved the problem!, I had numerated wrong my ligand in my initial pdb.
Thanx a lot to everyone for yours ideas.
Myriam
Carlos Simmerling <carlos.simmerling.gmail.com> escribió:
> 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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Received on Fri Jan 17 2020 - 08:00:02 PST
