[gmx-users] Carbohydrate MD Simulation

Nancy nancy5villa at gmail.com
Sat Aug 1 00:01:17 CEST 2009 

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)?




On Fri, Jul 31, 2009 at 5:47 PM, Justin A. Lemkul <jalemkul at 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 <jalemkul at vt.edu<mailto:
>> jalemkul at 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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>>
>>
>> ------------------------------------------------------------------------
>>
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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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