[gmx-users] gromos parameterisation in OPLS

[ANINDITA GAYEN]

Sir,

If i insert the hydrogen atoms in the first section of the itp file, where atomnames , atomtypes , nr, cgnr are displayed, wil it be wrong. Also, i was talking that, will the inclusion of "ffoplsaa.itp" will serve the bonded and nonbonded parameters if i supply the connectivities in all the bonds, pairs, angles and dihedral section by the atom numbers?

Thanks for the requested answers.

anindita




--- On Mon, 16/6/08, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] gromos parameterisation in OPLS
> To: aninditagayen at yahoo.co.in, "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Monday, 16 June, 2008, 9:29 PM
> Changing the atomtypes will only work if you have explicit
> inclusion of 
> all hydrogens in your PRODRG-generated topology.  Since the
> PRODRG 
> server outputs a GROMOS-based .itp file, this is unlikely
> unless your 
> molecule contains only polar or aromatic groups.  If
> we're still talking 
> about CHAPS or cholesterol, this will not be the case.  You
> will have 
> nonpolar groups that, within GROMOS, are atomtype CH1, CH2,
> etc., but 
> OPLS will not have these UA representations.
> 
> I'm not sure what you mean in the last sentence. 
> Nothing in this 
> process will be automatically generated for you. 
> You're building your 
> topology by hand.  Inclusion of "ffoplsaa.itp"
> will tell grompp which 
> parameters (bonded and nonbonded) apply to your molecule. 
> Calling 
> "ffoplsaa.itp" will not tell any Gromacs program
> to automatically detect 
> and generate bonds, dihedrals, etc. 
> 
> The only way to have "automatic" generation of
> these parameters is to 
> build an .rtp entry for your molecule that contains all of
> this 
> information as well, and process your structure with
> pdb2gmx.  This is 
> just as much work as building the topology yourself, I
> think.
> 
> -Justin
> 
> ANINDITA GAYEN wrote:
> > Hi,
> >
> > I came to know from the mailing list that if i only
> change the atomtype in the output itp file of PRODRG2 and
> put the charges as optimised by Gaussian; provided i
> include #include ffoplsaa.itp in the .top file of the new
> molecule and just keep the atom mumbers in [bonds],
> [pairs], [angles] and [dihedrals] as found in the the all
> atom pdb of PRODRG2, the resultant top file will be a top
> file in OPLS format. It was also stated there in the
> mailing list that for the atom numbers mentioned the opls
> staff will put the parameter values necccesary for the
> [bonds], [angles] etc.
> >
> > Is the approach right? 
> >
> >
> >
> >
> >
> >
> >       From Chandigarh to Chennai - find friends all
> over India. Go to
> http://in.promos.yahoo.com/groups/citygroups/
> >
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the
> list. Use the 
> > www interface or send it to
> gmx-users-request at gromacs.org.
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> >
> >   
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================


      Connect with friends all over the world. Get Yahoo! India Messenger at http://in.messenger.yahoo.com/?wm=n/