[gmx-users] Fwd: removing some atoms

[Elton Carvalho]

I am not sure how familiar with programming, but my usual approach is
to simply insert the molecules and then write a program that removes
the solvent residues whose atoms are too close to the protein.

Another approach would be to use gmx solvate to solvate your protein
as usual and then write a program/script to remove oil molecuels from
one side of the box (z > box_heigh/2 maybe?). In your place I'd try
this one.

On Mon, Nov 30, 2015 at 5:55 AM, João Martins <joaomartins139 at gmail.com> wrote:
> There are some automated tools for membrane insertion that you can probably
> modify for you use, but I would probably just try a manual insertion
> followed by a long equilibration. For the membrane insertion you have this
> tutorial which uses InflateGRO:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
>
> Like I said, for this specific case I would probably do it manually,
> probably with Pymol. You can load both structures, and move the protein to
> the desired position using the editing mode. Then, delete overlapping oil
> atoms and save the structure.
>
> Best regards,
> João Martins
>
>
>
> *Joao Martins*
>
> joaomartins139 at gmail.com
>
> On Mon, Nov 30, 2015 at 9:44 AM, James Lord <jjamesgreen110 at gmail.com>
> wrote:
>
>> Hi all,
>>
>> I sent this few days ago and I am still struggling with this, any
>> help,hints is highly appreciated.
>>
>>
>>
>>
>> ---------- Forwarded message ----------
>> From: James Lord <jjamesgreen110 at gmail.com>
>> Date: Thu, Nov 26, 2015 at 11:18 PM
>> Subject: removing some atoms
>> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>>
>>
>> Hi all,
>>
>> I have a oil slab and want to insert a protein so that almost half of the
>> protein is inserted into the oil and the other half is outside in the
>> vacuum. Is there any tools in Gromacs so that I can easily remove some of
>> the oil atoms and make a space for the protein insertion? My apology if it
>> seems a trivial question.
>>
>> Cheers,
>> James
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-- 
Elton Carvalho