this is a great use of mdgx, but I also recommend *always looking at the
structure validation report on RCSB* if that's where you got your PDB file.
It will show you any areas not included in the structure (look at "
Residues present in the sample, but not in the model, are shown in grey ").
it's well worth spending time looking at the report before doing any system
setup or MD.
On Tue, Jul 9, 2019 at 12:34 PM David Cerutti <dscerutti.gmail.com> wrote:
> This smells like a missing residue(s) problem--there is a loop or some
> other part of the protein that is not observed in the X-ray structure due
> to disorder. These residues have been omitted. Write the following input
> for mdgx:
>
> cat > mdgx.in << EOF
> &files
> -p <your prmtop>
> -c <your inpcrd>
> &end
>
> &configs
> count 1
> verbose 1
> maxcyc 2
> outbase 'Conf',
> write 'pdb',
> &end
> EOF
>
> Then run mdgx -O -i mdgx.in... this will apply the 'configuration sampling'
> protocol which is really for making large numbers of conformational
> variants of small molecules (I know oyu know this, I'm saying it for the
> listserv). Here, we're taking advantage of the checks it puts on each
> resulting configuration: it tells us where the strain was. The maxcyc 2
> won't converge, and mdgx will print no results (not even the 1 we asked
> for) because the sanity checks fail. (This is assuming that the problem is
> a missing few residues in the protein). Sure enough, here's the result at
> the bottom of the mdgx mdout file:
>
> - Configuration 1:
> Strain is 27322.3495 for bond C -N (4048, 4050)
> Strain is 35.0364 for angle CA -C -N (4045, 4048, 4050)
> Restraint binding atoms () strained to 0.0000
>
> So look at atoms 4048 and 4050--a peptide bond is stretch between some
> residues that look skipped. The atom numbering got a little jumbled when
> tleap created the topology, but I reproduced your error with the "bond of
> 8.882 between..." and we can run ambpdb -p [your topology] < [your
> coordinates] > [new pdb file] to see what the topology really looks like.
> Here are the aforementioned atoms in that structure:
>
> ATOM 4046 HA2 GLY 259 29.274 48.036 -30.126 1.00
> 0.00 H
> ATOM 4047 HA3 GLY 259 30.160 47.170 -29.179 1.00
> 0.00 H
> ATOM 4048 C GLY 259 30.907 49.072 -29.422 1.00
> 0.00 C
> ATOM 4049 O GLY 259 30.492 49.715 -28.456 1.00
> 0.00 O
> ATOM 4050 N ASN 260 31.807 49.055 -38.259 1.00
> 0.00 N
> ATOM 4051 H ASN 260 32.316 49.075 -39.131 1.00
> 0.00 H
> ATOM 4052 CA ASN 260 30.347 49.097 -38.308 1.00
> 0.00 C
>
> So, missing residues between GLY 259 and ASN 260.
>
> Dave
>
>
>
>
>
> On Tue, Jul 9, 2019 at 12:16 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > sorry I meant to visualize your prmtop and crd in something like VMD.
> >
> > On Tue, Jul 9, 2019 at 11:49 AM Anthony Bogetti <
> anthony.bogetti.gmail.com
> > >
> > wrote:
> >
> > > The pdb file was originally a dimer, but we removed one of the chains.
> > We
> > > tried adding in TER line at the end and it didn't fix the issue.
> > >
> > > How can I load prmtop and inpcrd files directly into leap?
> > >
> > > Thanks,
> > > Anthony
> > >
> > > On Tue, Jul 9, 2019 at 11:44 AM Carlos Simmerling <
> > > carlos.simmerling.gmail.com> wrote:
> > >
> > > > you might try to load in the prmtop and inpcrd generated by leap,
> since
> > > > that will show the bonds leap determined.
> > > > could you have a dimer without a TER line?
> > > >
> > > > On Tue, Jul 9, 2019 at 11:41 AM Anthony Bogetti <
> > > anthony.bogetti.gmail.com
> > > > >
> > > > wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > I'm trying to create a topology and coordinate file for a protein
> in
> > > > leap.
> > > > > I obtained the pdb file and added hydrogens and changed nothing
> else.
> > > > When
> > > > > I load the pdb file in tleap, everything seems fine but I'm getting
> > an
> > > > > error message that says:
> > > > >
> > > > > There is a bond of 8.882728 angstroms between: [Blank]
> > > > >
> > > > > It doesn't tell me what atoms this "bond" is between. What could
> be
> > > > > causing this?
> > > > > I've visualized my structure and everything looks fine.
> > > > > I'm using ff14SB and I've checked all of my atom names/types and
> they
> > > are
> > > > > correct.
> > > > >
> > > > > Thanks,
> > > > >
> > > > > Anthony Bogetti
> > > > > Graduate Student at University of Pittsburgh
> > > > > Advisor: Dr. Lillian Chong
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Received on Tue Jul 09 2019 - 10:30:01 PDT
