[gmx-users] Formyl parameters
shima_arasteh2001 at yahoo.com
Wed May 9 16:02:29 CEST 2012
OK, I have to build a .rtp file. But I'd like to know if I should make it corresponding to relation between.itp and .rtp files format?
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, May 9, 2012 3:58 PM
Subject: Re: [gmx-users] Formyl parameters
On 5/9/12 4:48 AM, Shima Arasteh wrote:
> 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?
No, you haven't. What you've defined now are two separate molecules, when in fact the formyl group needs to be an added moiety to your protein.
Dealing with this species can be done in one of two ways, both of which require an .rtp file. Whether or not making a formyl .rtp entry is appropriate is up to you based on the parameterization you have already done. I would be very surprised if the presence of the formyl group did not change some aspect (e.g. charges) of the amino acid to which it is connected. In this case, it is better in my mind to create an .rtp entry for the complete formylated amino acid, change residue and/or atom names as necessary in the .pdb file, and run the entire structure (with the formyl group) through pdb2gmx. The general workflow for doing all of this (in addition to information in the manual) can be found at:
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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