[gmx-users] Adding two peptides in a water box

Mon Sep 10 21:56:36 CEST 2007

Hi Guys,

Thank very much for your time trying to help me with this issue. 

It seems from all your answers that adding two identical peptides, separated by a certain distance from each other, and then put them into a water box with ions is a simple task. However, it is still puzzling me. Although, I have analized very carefelly all your suggestions and proved them, my problem still remain unsolved. 

My last .gro file, the one containing the two petides with water and ions, lacks the H in the N-term of the first protein, and the O in the C-term of the second protein. 

John,

You suggested to me to use the -label option, but forgot to tell me from which gromacs program tool. The pdb2gmx version I have (VERSION 3.3.1) does not contain such a label. This option (-label) exists in the editconf, but it did not solve the problem.  Could you be more specific and tell me, how to use this option -label and to which tools it is connected? Please, I will appreciate any simple example.

Lars and Mark,

I always read your emails, they have helped me a lot in many different occacions, but this time I could not figure out 
any simple solution from your recommendations. I've read the manual, particularly chapter 5, but still there are things that I can not put together; perhaps that is why I can not solve this "rather" simple problem.

Let me explain once again, what I am trying to do. Perhaps, I was not clear enough the first time I put my problem in the list:

I want to simulate the interaction between two identical proteins solvateed in water. I think, I am familiar with GROMACS, and I know how to prepare, run and analyze a single solvate peptide.

Thus, following the same procedures, I started preparing my simulation with the two identical proteins.

I start from the PDB file of protein_A.pdb. Creates the protein_A.gro and protein_A.top file.
I applied translation and rotations to the protein_A.gro file (edifconf) and creates a new protein_B.gro file that I named protein_B.gro
I assume that the protein_A.top file is the same for protein_B.gro, so I don't need to run pdb2gmx again.

Thus, at this point I have two .gro files and one topology file. So, how do I modified the .gro files and the .top file 
to clearly indicate that I have two chains in my composed system?

P.S. I also read the pdb2gmx -h very carefully and did not find any second alternative. The -[no]merge flag, that might indicates to be useful for this type of problem, did not work either.

Please, I need your HELP!

All the best,

Luciano

Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938

________________________________

From: gmx-users-bounces at gromacs.org on behalf of Sheyore Omovie
Sent: Sat 9/8/2007 12:36 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] Adding two peptides in a water box

Hi Luciano,
use the -label option to separately label the gro files (e.g A for the first peptide and B for the 2nd), before you cat them with an editor. pdb2gmx should now recognise them as separate molecules.
Rgds
John

> Date: Sat, 8 Sep 2007 15:43:33 +0200
> Subject: Re: [gmx-users] Adding two peptides in a water box
> From: Lars.Schaefer at mpi-bpc.mpg.de
> To: gmx-users at gromacs.org
> 
> > Hi Everybory,
> >
> > I would like to simulate the interaction between two separated peptides in
> > a water box. Every peptide needs to be N-and C-terminated. I have tried
> > different alternatives in order to create the corresponding GROMACS files
> > to start my simulation. I have used the GROMACS porograms tools as
> > described in the manual. However, I still have some problems and need of
> > your expeirences.
> >
> > This is what I do:
> >
> > 1.- I start from a pdb of one peptide.
> > 2.- Create the gro and top files. In this step I terminate the peptide
> > without any problem.
> > 3.- Apply corresponding translations and rotation to the existing gro file
> > (obtained in step 1) and create a new .gro file. This one is termed the
> > second peptide.
> > 4.- Cat them with an editor and save the result in a file named dimer.gro.
> > I can visualize it without any problem. So far, everything is going good.
> > 5.- HERE STARTS THE PROBLEM. I use dimer.gro as input to pdb2gmx to create
> > the new, dimer.top file. The pdb2gmx removes the hydrogens of the N-term
> > of one petide and the oxigen of the C-term in the second peptide.
> > Although, they are far apart.
> >
> > Does anyone know how to overcome this porblem?
> 
> Hi,
> why do you run pdb2gmx for the dimer? run it for the monomer, and then
> just put a "Protein 2" instead of a "Protein 1" (or however you name it)
> at the end of your topol.top file (just as is done for the water
> molecules, ions, etc).
> Lars
> >
> 
> > Thank in advance for you time.
> >
> > Ciao,
> >
> > Luciano
> >
> > Dr. Luciano Triguero College of Art and Science Department of Physics and
> > Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box
> > 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office:
> > 305-284-3938
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
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> 
> 
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