[gmx-users] Formyl parameters

Justin A. Lemkul jalemkul at vt.edu
Tue May 8 17:30:19 CEST 2012

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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