VMD-L Mailing List

From: Nathan Kern (nathan.kern_at_lehigh.edu)
Date: Wed Aug 18 2021 - 09:39:58 CDT

Dear Geo,

If it isn't in the CHARMM-GUI lipid library, then it is probably not in any
PDB either. That means you'll have to make the CHARMM36 residue topologies
and parameters yourself. You can look into FFTK, FFParam, Gaussian,
CGenFF/Paramchem, and probably a few others I'm missing.

While parameterization is much easier than it used to be, it can still be a
massive undertaking. I would confirm with your academic advisor that this
is really what you are supposed to be doing.

If you do manage to make the RTF/PRM, the CHARMM-GUI developers are usually
willing to add them to the CHARMM-GUI lipid library.

Nathan Kern

On Tue, Aug 17, 2021 at 5:48 PM Ropon-Palacios G. <groponp_at_gmail.com> wrote:

> Dear users,
>
> I need these types of lipids DPG3, DPG1, PAPI, PGPS. To create a bilayer,
> but in the charmm-gui I can't find them, so I have to build it manually,
> could you please tell me where I can find its structure in PDB and if the
> charmm36 force field has parameters for these.
>
>
>
> Greetings,
>
>
>
> Geo.
>
>
>
> --
>
> *Ropón-Palacios G. BSc., MSc. *
>
> Computational biophysicist,
>
> Associate Research,
>
> Laboratorio de Modelagem Computacional,
>
> Departamento de Ciências Exatas,
>
> Universidad Federal de Alfenas, Minas Gerais, Brasil.
>
> Phone: +51 935 055240.
>
> E-mail: groponp_at_gmail.com.
>
>
>
>
>
>
>
>
>