[gmx-users] Re: Re: Bonds break while Minimising using distance restraints
plmallip at mail.uh.edu
plmallip at mail.uh.edu
Thu Sep 4 01:21:23 CEST 2008
----- Original Message -----
From: Ryogo Sugitani <rsugitani at ucdavis.edu>
Date: Wednesday, September 3, 2008 5:46 pm
Subject: Re: [gmx-users] Re: Re: Bonds break while Minimising using distance restraints
To: plmallip at mail.uh.edu
> Latha,
>
> I'm not sure why there is 1-4 interaction between 6151 and 6160
> by just making distance restraint between 1703 and 1712
> (because they shouldn't make a physical bond...)
>
> but maybe adding space before and after distace_restraints
> (between brackets) might help?
> Also, check the trajectory on VMD.
> The warning is given, but md (or minimization) itself might be
> running fine...
>
> Other than this, I probably won't be able to help you any further.
>
> Also, please post it back to gmx-ml for me...
> (just reply to this message and change the address to gmx's list)
>
> Thanks,
>
> Ryogo
>
>
>
> On Wed, 03 Sep 2008 16:43:45 -0500, plmallip at mail.uh.edu wrote:
> > Hi Ryogo,
> >
> > Thanks
> for your suggestion. You are right. But, I did do the
> > energy minimization assuming the units are in nm But, I am
> still
> > facing the same problem of the residues to which I imposed
> distance
> > restraint breaking into fragments. I get this warning -
> 1-4
> > interaction between 6151 and 6160 at distance 1.387 which is
> larger
> > than the 1-4 table size 1.000 > nm. These are ignored for the
> rest of
> > the simulation. This
> > usually means your system is exploding.
> >
> > Do you have any other suggestions?
> >
> > Thanks & regards,
> > Latha.
> >
> > ----- Original Message -----
> > From: Ryogo Sugitani <rsugitani at ucdavis.edu>
> > Date: Wednesday, September 3, 2008 2:58 pm
> > Subject: Re: [gmx-users] Re: Re: Bonds break while Minimising
> using
> > distance restraints
> > To: plmallip at mail.uh.edu
> >
> >> Hi Latha,
> >>
> >> Since I cannot post it to the gmx ML directly for some
> reason,
> >> I'll just give this e-mail to you.
> >>
> >> I believe the unit for the distance used in
> distance_restraints
> >> is nm.
> >> So, you should change it to something like 1.15 1.20 1.20 for
> >> your setting.
> >> Currently you have 115A, 120A, 120A...
> >>
> >> Hope that helps,
> >>
> >> Best,
> >>
> >> Ryogo
> >>
> >>
> >> On Wed, 03 Sep 2008 13:27:06 -0500, plmallip at mail.uh.edu wrote:
> >>> Hi,
> >>>
> >>> There is no chance of
> steric
> >> clashes between 6151 & 6160. They
> >>> are seperated by 12 A. ("Warning: 1-4 interaction between
> 6151
> >> and
> >>> 6160 at distance 1.387 which is larger than the 1-4 table
> size
> >> 1.000
> >>> nm. These are ignored for the rest of the simulation. This
> >> usually
> >>> means your system is exploding") I cannot build the missing
> >> residues
> >>> without knowing the secondary structure. I am already
> running
> >> one
> >>> simulation with built residues. But, my ultimate goal is to
> >> run
> >>> dynamics with distance restraints.
> >>>
> >>> My sytem is
> an
> >> pentamer. Here is the toplogy file
> >>>
> >>> ; Include forcefield parameters
> >>> #include "ffG43a1.itp"
> >>>
> >>> ; Include chain topologies
> >>> #include "chnrc_A.itp"
> >>> #include "chnrc_B.itp"
> >>> #include "chnrc_C.itp"
> >>> #include "chnrc_D.itp"
> >>> #include "chnrc_E.itp"
> >>>
> >>> ; Include water topology
> >>> #include "spce.itp"
> >>>
> >>> #ifdef POSRES_WATER
> >>> ; Position restraint for each water oxygen
> >>> [ position_restraints ]
> >>> ; i funct
> >> fcx
> fcy fcz
> >>> 1
> >> 1
> 1000 1000 1000
> >>> #endif
> >>>
> >>> ; Include generic topology for ions
> >>> #include "ions.itp"
> >>>
> >>> [ system ]
> >>> ; Name
> >>> Protein in water
> >>>
> >>> [ molecules ]
> >>> ; Compound #mols
> >>>
> >>
> Protein_A 1
> >>>
> >>
> Protein_B 1
> >>>
> >>
> Protein_C 1
> >>>
> >>
> Protein_D 1
> >>>
> >>
> Protein_E 1
> >>>
> >>
> SOL 55419
> >>>
> >>
> NA+ 54
> >>>
> >>>
> >>> Thanks & regards,
> >>> Latha.
> >>>
> >>>>> plmallip at mail.uh.edu wrote:
> >>>>>
> >>>>> Hi Justin, thanks for your response. You are right. I get
> >> the
> >>>> following
> >>>>> message in the .job file
> >>>>>
> >>>>> "Warning: 1-4 interaction between 6151 and 6160 at
> distance
> >>>> 1.387 which
> >>>>> is larger than the 1-4 table size 1.000 nm
> >>>>> These are ignored for the rest of the simulation
> >>>>> This usually means your system is exploding"
> >>>>>
> >>>>> The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms
> >> are
> >>>> also from
> >>>>> the same residues). The distance between them is 12 A
> (there
> >>>> are 14
> >>>>> missing residues in between). My aim is to use distance
> >>>> restraints,
> >>>>> without building missing residues in between. Is there any
> >> way
> >>>> I can
> >>>>> overcome this warning why minimizing the system?
> >>>>
> >>>> It's very hard to say, because none of us knows what's in
> >> your
> >>>> system, topology,
> >>>> or how you built things :)
> >>>>
> >>>> You have some type of nasty steric clash that's driving
> atoms
> >>>> 6151 and 6160
> >>>> apart. Visualize the trajectory (.trr) to see if you
> >> can
> >>>> identify where things
> >>>> start to break down. I don't know if the distance
> >>>> restraint has anything to do
> >>>> with the problem or not.
> >>>>
> >>>> Is there a problem with building missing residues?
> That
> >>>> might make life quite a
> >>>> bit easier in the long run.
> >>>>
> >>>> -Justin
> >>>>
> >>>>>
> >>>>> Thanks & regards,
> >>>>> Latha.
> >>>>>
> >>>>>
> >>>>> > Dear colleagues,
> >>>>> >
> >>>>> > I need to use simple distance
> restraints of
> >> 12.5 A
> >>>> between two CA atoms
> >>>>> > of two residues. I am using the
> following
> >> lines in the
> >>>> .itp file
> >>>>> >
> >>>>> > #ifdef DDISRES
> >>>>> > [distance_restraints]
> >>>>> > ;ai aj type index type'
> >> low
> >>>> up1 up2 fac
> >>>>> > 1703 1712 1
> >>>> 0 1 11.5
> 12.0
> >>>> 12.5 1.0
> >>>>> >
> >>>>> > The first feww line of .mdp file for
> >> minimisation of
> >>>> protein alone is
> >>>>> >
> >>>>> > ; Preprocessing
> >>>>> > ;
> >>>>> >
> >>>>
> >>
> title = ${MOL}
> >>>>> >
> >>>>
> >>
> cpp = /lib/cpp ;Preprocessor
> >>>>> >
> >>>>
> >>
> define = -DDISRES ;For cg, and also steep
> >>>>> >
> >>>>>
> >>>>> You are not actually applying your distance
> restraint.
> >>>> If you have "#ifdef
> >>>>> DDISRES," then you would have to "define = -DDDISRES" in
> the
> >>>> .mdp file.
> >>>>> What
> >>>>> you probably meant to define was "#ifdef DISRES" in the
> topology.>>>>>
> >>>>>
> >>>
> >>>> After minimisation, the restarined residues & the adjacent
> >>>>> > bonds break. This results in fragmnets
> -
> >> residues
> >>>> alone, peptide bond
> >>>>> > alone and the rest of the protein. The
> >> distance
> >>>> restrained residues
> >>>>> > seems to try to move towards each
> other (6.04
> >> A after
> >>>> minimisation) and
> >>>>> > this might have caused fragmentation.
> I tried
> >> to use
> >>>> various upper and
> >>>>> > lower values for bond length so as to
> increase
> >>>> flexibility. But, still I
> >>>>> > end up in the fragments.
> >>>>> >
> >>>>>
> >>>>> Bonds don't break in classical MD, this is just an
> artifact
> >> of
> >>>>> visualization,
> >>>>> probably from nasty steric clashes within your structure.
> >>>>>
> >>>>>
> >>>>>
> >>> Some
> >>>> of the suggestions in the archive says VMD doesn't show
> >>>>> > bonds if they r above threshold value.
> When I
> >> checked
> >>>> the distances
> >>>>> > between the atoms, one of them is
> really long
> >> CO-CA
> >>>> bond 3.23 A
> >>>>> > (normally its 1.59A). This means the
> bond is
> >> no longer
> >>>> there.> >
> >>>>>
> >>>>> No, the bond is there, VMD just isn't smart enough to see
> it
> >>>> :) You are
> >>>>> probably well on your way to an explosion if you try to
> >>>> constrain bond
> >>>>> lengths
> >>>>> with LINCS, however.
> >>>>>
> >>>>> -Justin
> >>>>>
> >>>>>
> >>>>> -----------------------------------------------------------
> --
> >> --
> >>>> ---------
> >>>>>
> >>>>> _______________________________________________
> >>>>> gmx-users mailing list gmx-users at gromacs.org
> >>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
> >>>>> Please search the archive at http://www.gromacs.org/search
> >>>> before posting!
> >>>>> Please don't post (un)subscribe requests to the list. Use
> >> the
> >>>>> www interface or send it to gmx-users-request at gromacs.org.
> >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>>>
> >>>> --
> >>>> ========================================
> >>>>
> >>>> Justin A. Lemkul
> >>>> Graduate Research Assistant
> >>>> Department of Biochemistry
> >>>> Virginia Tech
> >>>> Blacksburg, VA
> >>>> jalemkul[at]vt.edu | (540) 231-9080
> >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>>>
> >>>> ========================================
> >>>
> >>> _______________________________________________
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> the
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> >>
>
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