[gmx-users] Re: Bonds break while Minimising using distance restraints
plmallip at mail.uh.edu
plmallip at mail.uh.edu
Thu Sep 4 01:30:53 CEST 2008
Hi,
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?
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.
>Then, are you correctly applying "define = -DDDISRES" in your .mdp as I
>suggested previously?
I did correctly use the -DDDISRES, as suggested by you, which is as follows:
title = ${MOL}
cpp = /lib/cpp
define = -DDDISRES
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
>
> ========================================
>
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