[gmx-users] How to proceed with molecule.itp file

[Sotirios Dionysios I. Papadatos]

Hi, 
This indeed begins to clarify things but just to make sure I got it right. 
I want to simulate only a specific molecule from a protein, meaning I took the initial protein and deleted everything but the molecule. 
So I use the pdb2gmx to the molecule, I edit the topol.top that is produced (even in error a .top file is produced) and then I replace everything from the .itp file that I made.?
Then I continue with the grompp command?
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Cara Kreck <cara.kreck at student.curtin.edu.au>
Sent: Thursday, May 21, 2015 1:59 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] How to proceed with molecule.itp file

Hi Sotirios,

You need to either edit the .top file produced by pdb2gmx or make your own from scratch. You only need the pdb2gmx output if your system includes standard amino acids.

If you have both a standard protein and a non-standard molecule, you should make a .pdb file with just the protein to use with pdb2gmx. I would then recommend you remove all the .top specific parts of this file and convert it to a .itp file for just the protein. Then make your own .top file using the bits you removed and link everything together. Alternatively you can just add to the include and molecule sections at the end of pdb2gmx's .top file.

If you don't have any protein, don't bother with pdb2gmx at all.

Here's an example DIY .top file:

; Forcefield files
#include "gromos53a6.ff/forcefield.itp"
#include "./lipids_vdw.itp"

; Parameter set for DOPC
#include "./dopc.itp"

; Include DMSO topology
#include "./dmso.itp"

; Include water topology
#include "spc.itp"

[ system ]
; Name
128 DOPC in DMSO solution

[ molecules ]
; name     number
DOPC          128
DMSO          496
SOL          7573


Make sure you use the molecule names defined in your .itp files and list the molecules in the same order that they appear in your coordinate file.

Hope that helps,

Cara


> From: si.papadatos at edu.cut.ac.cy
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Date: Thu, 21 May 2015 07:13:00 +0000
> Subject: [gmx-users] How to proceed with molecule.itp file
>
> Hi,
>
> I have made a molecule.itp file according to the chapter 5 of Gromacs Manual and existing entries in the ff directory I want to use.
>
> My problem is that I don't know how to continue, in theory I have to include it in the .top file but a .top file is produced by pdb2gmx which I cannot use because there isn't an entry in .rtp.
>
> Please help
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