[gmx-users] Protein pore collapse during simulation.

[Justin Lemkul]

On 1/24/20 2:15 AM, Yogesh Sharma wrote:
> Sir,
>   If i want to use charmm gui generated assembly for simulation in gromac
> forcefield. How can i extract berger lipid parameters (i.e lipid.itp
> according to yout tutorial) corresponding to charmm nomenclature? so that i
> can modify my forcefield in accordance.

You would have to rename the atoms in the coordinate file.

> my ultimate aim is to simulate membrane protein with a ligand. whose
> parameters are only available in gromacff (ATB). #ligand contain metalloid
> atoms.

You're making a big tradeoff here, as the Berger parameters are very 
inaccurate compared to modern lipid parameter sets. Metalloids are 
generally not available in biomolecular force fields, though. At least 
look at more recent GROMOS parameter sets rather than the Berger lipids.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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