[gmx-users] GMO simulation

[Justin Lemkul]

On 4/14/19 1:51 AM, RAHUL SURESH wrote:
> 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

If you already have coordinates and an .itp file, then preparing the 
system is straightforward. You do not need pdb2gmx and you can prepare 
the topology by hand. I doubt that my membrane tutorial is particularly 
helpful, however this one may be more useful as it involves creating a 
topology by hand and placing a protein in an aqueous layer:

http://www.mdtutorials.com/gmx/biphasic/index.html

>> 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.

That's not true - a modified force field can be placed in the working 
directory and pdb2gmx will actually read it first and put it in the 
selection list. Modifying force field files in the working directory is 
the preferred method in case something goes wrong; then the files in 
$GMXLIB do not get messed up.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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