Hi Thomas,
Let me add a brief response: Lipid11 and Lipid14 are compatible with NAMD.
Jason gave a good description of the 1-4 scaling factors. Lipid11 and Lipid14 use consistent scaling factors: i.e. SCEE=1.2 and SCNB=2.0. These are defined in Amber parameter "dat" files in the dihedral section in the comments. These are in turn saved in the prmtop input file. The only exception in Lipid11 is the head group phosphoinisitol (PI) which uses some GLYCAM parameters. In the future, there may be other exceptions as we add more glycolipids to the Amber lipid force field.
Amber has supported mixed scaling factors for some time (Amber >11).
As for pre-equilibrated structures, we are currently building a set of structures to be included with Amber or provided on the web site. We are planning to have the Lipid14 bilayer types of different sizes with optional hydration. It would be good to include bilayers with cholesterol as well.
All the best,
Ben Madej
UCSD Chemistry and Biochemistry
SDSC
________________________________________
From: Thomas Evangelidis [tevang3.gmail.com]
Sent: Wednesday, June 04, 2014 4:03 AM
To: AMBER Mailing List
Subject: Re: [AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10
Thank you Jason and Hannes! I guess by putting the following in my NAMD
.conf file I can run a protein-membrane simulation with the lipid11 or
lipid14 ff without carbonhydrates. Lipid11/14 does not use different
scaling factors than the amber ff, right?
exclude scaled1-4
1-4scaling 0.8333;# must be 1/scee, where scee is the
electrostatic scaling factor in AMBER
scnb 2.0 ;# VDW 1-4 scaling factor, required for AMBER
ff (although the default value is the same)
On 4 June 2014 13:07, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
> On Tue, 3 Jun 2014 17:58:11 -0400
> Jason Swails <jason.swails.gmail.com> wrote:
>
> > He didn't know
> > > exactly though what happens. Aren't these parameters defined
> > > explicitly in the .prmtop file so that NAMD could know how to
> > > compute the vdW and electrostatics correctly, or does the code
> > > override them?
> > >
> >
> > My guess is that NAMD ignores the SCEE_SCALE_FACTOR and
> > SCNB_SCALE_FACTOR sections of the prmtop and simply uses scee and
> > scnb as input by the user. But that may have changed in recent
> > versions.
>
> I have just tested this with today's CVS version of namd and it still
> ignores those flags.
> --
> Scanned by iCritical.
>
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>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Wed Jun 04 2014 - 14:00:03 PDT
