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>> 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> | (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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