as I mensioed before, the program is not identifying the
the SG:140 CG:211, I think it is not identifying gama
atoms......I dont know that how i am writing the gamma
atom is wrong ???
If i removed these lines from the restrain file, the
program is getting core dumped.
can you please help me out this problem.
Thanking you
regards,
Praveen
On Wed, 17 Nov 2004 16:32:54 -0800
wrote:
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Subject: Re: RE: [modeller_usage] wrong topology for
the ligand?
To: Youbin Tu <>
Cc:
Message-ID: <>
Content-Type: text/plain; charset=us-ascii
On Wed, Nov 17, 2004 at 05:25:09AM -0500, Youbin Tu
wrote:
Thanks for your reply, which help me a lot.
But for my specific situation, the ligand I am trying
to use is
phenacetin which did not exist in the template pdb
file. Or to say, we
created it so as to make it docked in the active site by
using some NMR
restraints. We expected to see some interactions between
the ligand and
the active site which will make the active site show a
differnt look
from what it is when no ligand is bound.
Yes - if there is no template, you will have to define
parameters for
the ligand.
Now I was really confused, if the ligand can not have
correct
connectivity, how can we expect to see the interactions
between the
ligand and the enzyme?
You misunderstand me. Modeller knows the connectivity -
it reads it from
the topology file - but it doesn't write it to the final
model PDB file,
so your PDB viewer cannot read the connectivity.
Again, why the ligand does not show correctly, you
know , we build
the phenacetin in Builder module in InsightII and
output it as a RTF
file, then append it to the top_heav.lib file.
The RTF file only defines the topology. It doesn't
define the
parameters. These need to be put into par.lib. This is
the case for any
molecular mechanics package, not just Modeller.
Another question is whether does the RTF file provide
enough
connectivity information for the ligand?
Certainly. All connectivity for the ligand is included
in the RTF
(residue topology file) but you need the parameters as
well. If
InsightII has parameters defined for your ligand, you
will need to save
them as well, and put them into Modeller's par.lib file.
Note that the topology only defines bonding
interactions, i.e. covalent
bonds within the ligand or protein. Interactions between
the ligand and
the protein are non-bonding, and are not described here
- you'd use VDW
or electrostatic interactions for that.
Or is it because of the special restraints we applied in
MODELLER which
make the connectivity changed?
They won't change your topology, but of course, if you
have a bond
interaction which clashes with a user restraint,
Modeller will try to
Subject: Re: RE: [modeller_usage] wrong topology for
the ligand?
To:
Message-ID:
<>
Content-Type: text/plain; charset=ISO-8859-1
Quoting Youbin Tu <>:
Hi Alicia, Ben:
Thanks for your reply, which help me a lot.
But for my specific situation, the ligand I am trying
to use is
phenacetin which did not exist in the template pdb
file. Or to say, we
created it so as to make it docked in the active site by
using some NMR
restraints. We expected to see some interactions between
the ligand and
the active site which will make the active site show a
differnt look
from what it is when no ligand is bound.
You have used NMR perturbation data to dock a ligand
into the active site? You
could simulate a ligand-induced conformational change in
the receptor just by
doing some MD on your complex. I recommend NAMD.
However, AMBER will probably
work better for you since your compound has an aromatic
ring.
Now I was really confused, if the ligand can not have
correct
connectivity, how can we expect to see the interactions
between the
ligand and the enzyme? I mean how the follwong
refinement steps which
is involved with minimization and molecular dynamics
correctly dealt
with the ligand and the interaction between the ligand
and the enzyme?
MD packages rely on complete topology/parameter sets.
You can use XPLO2D to
predict a lot of this information. However, be aware
that the values are
completely derived from the pdb file and will need to be
edited. Charges will
also need to be added.
Again, why the ligand does not show correctly, you
know , we build
the phenacetin in Builder module in InsightII and
output it as a RTF
file, then append it to the top_heav.lib file. The
molecule looks very
reasonable in InsightII, but after calculation by
MODELLER , the ligand
looked weird. So, any other program can view RTF file so
as to have a
check the connectivity of the ligand is reasonably good
or not? Or if
the parameters are incomplete, how to make it complete?
Although we have InsightII, I have never built an RTF
file with it. I'm guessing
it works similar to XPLO2D. Therefore you will most
certainly have to edit angle
and charge terms. However, you'd think that bonding
would be correct.
Another question is whether does the RTF file provide
enough
connectivity information for the ligand? Or is it
because of the
special restraints we applied in MODELLER which make
the connectivity
changed? You know,we even tried to use the ligand
without any
restraints, the result still looked weird?
To check if your RTF file provides correct connectivity,
pass it through X-PLOR
along with your pdb file to produce a psf. You can then
view your psf file in
VMD to make sure your connectivities are correct.
Otherwise just go through the
topology manualy.
Basically, we just want to build a new ligand with
some experimental
restraints in the active site of a enzyme. If the ligand
looked werid,
we have to doubt whether the interaction between the
ligand and the
enzyme is reliable or not? So, we have to know which
step create this
problem?
If you already have the structure of the protein you are
docking to then I
wouldn't recommend using MODELLER to dock your ligand
and observe ligand-induced
confomrational changes. Do MD.
1. building the ligand (RFT file)? We did not give
enough connectivity
information?
2. running MODELLER? Since there is no restraints to
confine the bond
or angles for the ligand or the restraints are
conflicting with each
other which make the ligand broken?
3. outputting file from MODELLER? Assumed that all the
above is good,
the only problem is that MODDLER only give the
cooridinates of the
atoms instead of the relationship ( connectivity)
between atoms?
Hope I have well explained my problems? And I also
attached my RTF
file for phenacetin.
Finally, thanks for your guys' kind help. Anyone's
reply in this
topic will be highly appreciated.
Hope for the best.
youbin
Sorry I didn't go through your RTF file but its
laborious work even with the
smallest of compounds. Best create the psf file and then
visualize it in VMD.
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