[gmx-users] How to parameterize glucose

[Justin Lemkul]

On 3/17/13 7:32 PM, dreda wrote:
> I'm trying to setup a simulation of 2 molecules of beta-D-glucose in vacuum
> at 100k. I'm using the OPLS/AA force field, have a pdb file that looks good
> in VMD, and have started creating the .itp file. I've described the bonds,
> pairs, and angles but am having difficulty completing the parameterization:
>
> 1. If I run grompp, I get the "no default angle types" error for the angle
> C1-O-H, where C1 refers to carbon-1, bonded to the O in the ring. If I
> comment out just that angle in the .itp file, grompp runs without problems.
> I assume this means the OPLS force field doesn't have an angle type
> corresponding to that part of the molecule. Why is this and what should I do
> about it?
>

No force field is guaranteed to accommodate any arbitrary molecule.  Most were 
designed around proteins and nucleic acids and later extended for other small 
molecules, lipids, etc.  You'll have to determine or derive suitable parameters 
for this angle if OPLS does not natively supply it.

> 2. I don't know how to specify dihedrals and improper dihedrals for glucose.
> What's the best place to learn this?
>

Chapter 5 in the manual is where all elements of the topology are described.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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