Nancy wrote:
High-throughput "in silico" screening (e.g. for ligand-protein binding)
has been performed on a number of systems. How are such automated
simulations performed (I assume they utilize molecular dynamics)?
I doubt that large classes of ligands have been done effectively with MD.
Docking is better suited to finding initial bound configurations, after which MD
can be useful in analyzing interactions over time.
Assumptions can be cleared up by reading Methods sections. If anyone has a
method for using unbiased MD to demonstrate ligand binding in large classes of
ligands, I'd love to know about it.
-Justin
On Fri, Jul 31, 2009 at 5:47 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Nancy wrote:
If it necessary to manually create force field parameters for
each molecule, then how can one run a simulation involving a
number of arbitrary molecules (e.g. a set of mono and
disaccharides) for which there are no existing force fields?
Do you know of any other MD software package that is capable of
running simulations on arbitrary molecules without having to
"piece together" a force field for each molecule?
Indeed it would be nice if there was a software package that would
parameterize your molecule, validate said parameters, then run a
meaningful simulation with all the proper conditions. Maybe it
could even make coffee...
All kidding aside, the answer is no. It is the job of the user to
generate and validate parameters when none are available. A proper
topology is perhaps the most important part of setting up a simulation!
There are some methods for doing some of this in an automated
fashion (i.e., RESP charge derivation, antechamber with GAFF, etc).
But the hard truth comes down to one simple fact - if no parameters
are already available, you must do that work. It is hard, but
necessary. Have a look at the Gromos96 force fields; they contain
some monosaccharide building blocks that should give you a
reasonable starting point.
-Justin
Thanks,
Nancy
On Fri, Jul 31, 2009 at 4:53 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Nancy wrote:
Hello,
I am trying to run a MD simulation on trehalose (glucose
disaccharide) in water. I obtained the PDB file from the
URL:
http://www.rcsb.org/pdb/files/ligand/TRE_model.pdb .
When I run
pdb2gmx on the PDB file:
pdb2gmx -f TRE_model.pdb -o TRE_model.gro -v
I chose force field 5 (OPLS) from the list:
Select the Force Field:
0: GROMOS96 43a1 force field
1: GROMOS96 43a2 force field (improved alkane dihedrals)
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6: [DEPRECATED] Gromacs force field (see manual)
7: [DEPRECATED] Gromacs force field with hydrogens for NMR
8: Encad all-atom force field, using scaled-down vacuum
charges
9: Encad all-atom force field, using full solvent charges
And I received the following error message:
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.5
Source code file: pdb2gmx.c, line: 429
Fatal error:
Atom C1 in residue TRP 1 not found in rtp entry with 24 atoms
while sorting atoms
-------------------------------------------------------
Well, pdb2gmx thinks that TRE is tryptophan, so it's looking to
complete a TRP building block. Furthermore, your procedure is
undoubtedly going to fail. Force fields and pdb2gmx are not
magic;
they are not equipped to handle any arbitrary molecule you
may want
to simulate. None of the force fields provided with Gromacs will
contain information for trehalose by default. There is
information
for glucose in some of the force fields (check the .rtp
files), and
you may be able to piece trehalose together from that
information.
Otherwise, you will have to go through the *very difficult and
time-consuming* process of parameterization:
http://oldwiki.gromacs.org/index.php/Parameterization
-Justin
Please help.
Thank you,
Nancy
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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