[Fwd: Re: [gmx-users] [Fwd: Grompp error (no default RB dihedral)]]

[David]

-------- Forwarded Message --------
From: Xiaoming Zhang <xzhang at artsci.wustl.edu>
Reply-To: xzhang at artsci.wustl.edu
To: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] [Fwd: Grompp error (no default RB dihedral)]
Date: Tue, 14 Jun 2005 12:11:46 -0500 (CDT)
David,

Thank you very much for your help.  I tried to find a reasonable C-C-C-H 
dihedral for AIB in ffoplsaabon.itp.  what I found are several dihedrals that 
I might use for AIB, such as C-C-C-H in "Hydrocarbon all-atom", C-C-C-H 
in "ketone", and C-C-C-H in "chi-1 peptides AA".  There is no exact C-C-C-H 
dihedral for AIB in ffoplsaabon.itp.  So I used C-C-C-H in "Hydrocarbon all-
atom" for AIB in my MD simulation (2ns).  I noticed that my peptide was 
trapped into some kind of local minimum and no significant conformational 
change was observed.  I increased the simulation temperature from 300K to 350K 
and 400K respectively, I found that peptide was trapped into different 
minimum.  The simulation has been done in OPLSAA with explicit DMSO.  The 
peptide I used is D-Pro-Ala-Ala-Aib-Ala.  I also run simulation on D-Pro-Ala-
Ala-Ala-Ala in explicit DMSO using Gromacs and that gave me quite reasonal 
results.  I guess maybe I used the wrong parameters for C-C-C-H dihedral in 
AIB?

Best,
Xiaoming



> On Wed, 2005-06-08 at 07:26 +0200, David wrote:
> > -------- Forwarded Message --------
> > From: Xiaoming Zhang <xzhang at artsci.wustl.edu>
> > Reply-To: xzhang at artsci.wustl.edu
> > To: David van der Spoel <spoel at xray.bmc.uu.se>
> > Subject: Grompp error (no default RB dihedral)
> > Date: Tue, 7 Jun 2005 17:41:33 -0500 (CDT)
> > Dear Dr. Spoel,
> > 
> > I am a graduate student at Washington University in St. louis.  Currently 
I am 
> > working on the MD simulation in oplsaa ff using GROMACS.  My peptide has 
> > an "AIB" residue.  GROMPP complained that the six dihedrals (c-c-c-H) in 
> > dimethyl group of AIB are not default RB type.  I was wondering whether it 
is 
> > ok to ignore that warning and how to add parameters for those dihedrals if 
I 
> > want to fix the problem.
> edit the AIB entry in ffoplsaa.rtp to add the correct dihedrals. You
> will find those in ffoplsabon.itp
> 
> If you make it work (and it behaves well) then please report the update
> AIB entry back to the list (or to me).
> > 
> > Thank you very much,
> > 
> > Xiaoming Zhang
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++