[gmx-users] Re: Bonds break while Minimising using distance restraints
Justin A. Lemkul
jalemkul at vt.edu
Thu Sep 4 02:33:58 CEST 2008
plmallip at mail.uh.edu wrote:
> My protein has 5 chains. 1703 & 1712 are the numbers from chainC.itp
> file. This includes the distance restraints -
>
> #ifdef DDISRES
> [ distance_restraints ]
> ;ai aj type index type' low up1 up2 fac
> 1703 1712 1 0 1 1.15 1.20 1.25 1.0
> #endif
>
> 6151 & 6160 atoms are the numbers from .gro file reported by the .job
> file. 6151 is N of residue 584 and 1703 is CA of the same redsidue.
> Residue 584 & 585 are placed have 14 residues missing between them. 6160
> is N of residue 585 & 1712 is the corresponding CA.
So you have an incomplete protein backbone, with some odd numbering. What
command did you give pdb2gmx to generate this topology? Did you use the
-missing flag? If so, the topology may be badly broken and unexpected bonds
defined. Look closely at your [ bonds ] section in "chain_C.itp" in case you
have some bonds that you are not expecting!
Do you have complete residues for each of those that contain atoms 6151, 6160,
1703 and 1712? The non-sequential numbering (with 4000-atom separation!) does
not indicate that these atoms should be in the same residues.
Is your structure one that is available in the PDB? Perhaps it would be much
easier to diagnose this if I could see the structure. I'd be willing to have a
look at your structure file, if you'd like to send it to me privately. I'm
somewhat intrigued as to what the problem is :)
I would be willing to bet that there is something within that chain topology
that is causing mdrun to find a 1-4 interaction between atoms 6151 and 6160.
-Justin
>
>
> Thanks & regards,
> Latha.
>
>
> ----- Original Message -----
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Date: Wednesday, September 3, 2008 5:36 pm
> Subject: Re: Bonds break while Minimising using distance restraints
> To: plmallip at mail.uh.edu, Gromacs Users' List <gmx-users at gromacs.org>
>
> >
> >
> > plmallip at mail.uh.edu wrote:
> > > Hi Justin,
> > >
> > > Thanks for your prompt
> > suggestions. I hope I didn't cause any
> > > sort of inconvenience by E-mailing you directly.
> > >
> >
> > I say this constantly - it is always better to keep the
> > discussion on the list
> > so that, if I don't have the complete right answer (which
> > happens often!)
> > someone else can weigh in and help out. It is also helpful
> > to complete
> > discussions in the archives. There's nothing more
> > frustrating than finding your
> > exact problem in the archives, only to find out that the thread
> > dies off without
> > a solution :)
> >
> > > >I thought you were applying a 12-nm distance restrain
> > to atoms in the
> > > 7000's, so
> > > >I'm confused as to why atoms615 1 and 6160 should be 12
> > nm apart
> > > (assuming, of
> > > >course, that you meant to say nm instead of A :)
> > >
> > > I am sorry for the confusion.
> > The atoms are separated by 12 A (1.2
> > > nm). The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms
> > are also
> > > from the same residues). These are the residues that looks as
> > if they
> > > are no bonds between them. ( residues alone, peptide bond
> > alone and the
> > > rest of the protein).
> >
> > How is it that atoms that are 900 indices apart are in the same
> > residues. I
> > don't understand. Do you mean that all four of these atoms
> > are in the same
> > residue? Then they definitely aren't amino acids!
> > Are these two separate
> > residues bridged by a distance restraint, that you are
> > considering one residue?
> > Is there some bond defined in the topology between *any*
> > of these atoms?
> >
> > >
> > > While doing grompp I get the following "removed 1 distance
> > restraints".
> > > Does this mean, the distance restraint isn't imposed at all?
> > >
> >
> > That would be a pretty clear indication to me that distance
> > restraints are not
> > being applied.
> >
> > > I corrected the distance restraints I used as
> > >
> > > #ifdef DDISRES
> > > [distance_restraints]
> > > ;ai aj type index type' low up1
> > up2 fac
> > > 1703 1712 1 0
> > 1 1.15 1.20 1.25 1.0
> > > #endif
> > >
> >
> > Then, are you correctly applying "define = -DDDISRES" in your
> > .mdp as I
> > suggested previously?
> >
> > http://www.gromacs.org/pipermail/gmx-users/2008-September/036136.html
> >
> > -Justin
> >
> > > I endup with the same error. Is there any possible way to get
> > over this
> > > problem?
> > >
> > > I appreciate your help in this regard.
> > >
> > > wamr regards,
> > > Latha.
> > >
> > >
> > > > 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.
> > >
> > > Are you sure you are identifying the correct atoms? A 1-
> > 4 interaction
> > > involves
> > > atoms that are very close together (in fact, three bonds
> > away). Are you
> > > saying
> > > that they are separated by 12 A (1.2 nm) or by 12 nm? If
> > they are
> > > starting 12 A
> > > (1.2 nm) away, then the error message still makes sense.
> > If they are 12 nm
> > > away, then I suspect that some sort of bond or restraint is
> > being applied
> > > improperly.
> > >
> > >
> > >
> > > I thought you were applying a 12-nm distance restrain to atoms
> > in the
> > > 7000's, so
> > > I'm confused as to why atoms615 1 and 6160 should be 12 nm
> > apart
> > > (assuming, of
> > > course, that you meant to say nm instead of A :)
> > >
> > > -Justin
> > >
> > > >
> > > > 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
> >
> > --
> > ========================================
> >
> > 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
> >
> > ========================================
> >
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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
========================================
More information about the gromacs.org_gmx-users
mailing list