[gmx-users] GMO simulation

[RAHUL SURESH]

On Sun 14 Apr, 2019, 11:15 AM Ayesha Fatima, <ayeshafatima.69 at gmail.com>
wrote:

> Dear All,
> I have a glyceryl monooleate 100 molecule assembly. I want to pull a
> peptide like molecule through it. I have obtained the forcefield files
> from *Boeckmann,
> Rainer website.*
> I followed the Bevan Lab KAlp15 tutorial to build topology of lipids but
> got stuck as the force field obtained from Rainer website and put in the
> working directory, the path to working directory does not appear in the
> list of forcefields.
> i prepared my molecule using 54a7 forcefield implemented in ATB server. i
> got the itp files and prepared the gro file using editconf
> My question is to anyone who has done the glycerol simulation using
> gromacs. please help with the exact procedure to develop the simulation
> files. Should I add the 54a7 forcefield with to the OPLSAA updated
> forcefield by Prof Rainer or vice versa? I also have a peptide like
> molecule to pull through the GMO membrane. Any one can help guide through
> this?
>

Hi

You must add the ff in Ur gromacs directory and not in Ur working
directory.

For example, use/local/gromacs/share/gromacs/top

And that will reflect the FF in pdb2gmx.

>
> Thank you in anticipation
> Ayesha
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