[gmx-users] Formyl parameters

Shima Arasteh shima_arasteh2001 at yahoo.com
Wed May 9 10:48:57 CEST 2012

Oh my god! :-)

The situation seems going complicated!  :-( 

Let me explain what I'm gonna do in detail:

I have formyl residue as the N-terminus in my protein (.pdb file) ! As you know, the topology database in CHARMM27  doesn't have formyl. So I got its parameter as an .itp file through  swissparam site. Now I need to include the parameters in the top file. But don't know it well! I just did such as this:

1. seperating the formyl residue from my .pdb file.

2. run pdb2gmx to get top file ( for the .pdb file which doesn't have formyl )

3. include the formyl .itp file in my top file 

Now please let me know if I've done correctly?


 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, May 8, 2012 8:00 PM
Subject: Re: [gmx-users] Formyl parameters

On 5/8/12 11:25 AM, Shima Arasteh wrote:
> Dear gmx users,
> My .pdb input file has a formyl group which is not defined in CHARMM27 and
> CHARMM36. So I got its .itp file through swissparam. Now I want to use its
> parametrs. As I read in gromacs.org , I need to include this .itp in .top file.
> How does it come when I have not got any .top file yet?
> Anybody can suggest me how I can use .itp file and solve my problem?

The solution to the problem depends on what you need to do.  Your use of the term "formyl group" seems to imply that it is an adduct to some existing molecule, i.e. C(=O)H.  If this is correct, then you need to do one of two things:

1. Add the formyl group as an entry in the relevant .rtp file (using the parameters contained in the .itp file) so it can be used as a building block on its own.

2. Incorporate the parameters into an existing residue that it is modifying, though if this is the case you should be parameterizing a new residue rather than a formyl moiety.

If the "formyl group" is actually a standalone molecule, i.e. formaldehyde or formate, then the solution is certainly as simple as adding an #include statement to the .top file.  The source of the .top also depends on what you're doing.  It can be generated by pdb2gmx in the case of a macromolecule or it can be written by hand in a text editor in simple cases.

In any event, if you need further help, you need to post considerably more information about what you're trying to achieve.  I can probably guess a few more potential scenarios, but I'd rather not waste a lot of time ;)


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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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