AMBER Archive (2007)

Subject: Re: AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed May 30 2007 - 12:50:05 CDT

I'd suggest tracking N-CA-C-N instead of HA-CA-C-O, it is the
same dihedral but the former is the definition of psi and you can then
think about it more easily in phi/psi terms.

also, have you run it without the glycam part? you might check in
the resulting prmtop to see if using glycam has modified the phi/psi
parameters for the peptide.

it's not really clear to me that what you are seeing is because of glycam
or just some backbone flexibility in the peptide (whether it is correct or
not)
carlos

On 5/30/07, Andrew Borgert <borg0109_at_umn.edu> wrote:
>
> I am attempting to run unrestrained MD on a small glycopeptide ( 9 amino
> acid and 4 GalNAc) in explicit solvent using parm94, glycam04l (the
> latest version) and AMBER8, however I am having problems with backbone
> stability at the first glycosylated threonine. The most obvious symptom
> of the instability is that the HA-CA-CO-O dihedral angle in the first
> threonine switches from ~ -130 to ~ 60 degrees after several
> nanoseconds, resulting in what could best be described as a 'kink' in
> the glycopeptide.
>
> Some important notes about the system and MD parameters:
>
> This is definitely not a switch to the cis configuration
>
> 1 fs timestep.
>
> The glycosylated threonine in question is preceded by two prolines, and
> followed by 3 more glycosylated THR's and then the rest of the peptide.
>
> The starting structure was initially produced with xplor using NOE and
> coupling data and approximates a beta-strand across the THR's.
>
> I am using a truncated octahedron box with a 'radius' of 9 angstroms
> along with TIP3 water, PME and constant pressure.
>
> The system temperature was run up to 300K over 20 ps with weak
> restraints on the glycopeptide
>
> I have attempted to stabilize the peptide by adding bulk (in this case 4
> Ala's on each end) to the glycopeptide, but without success.
>
> Run using 4 processors of a SGI/Linux machine
>
> here is the sander input file for the unrestrained dynamics:
>
> &cntrl
> imin=0,
> irest = 1,
> ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0,
> cut = 10,
> ntr = 0,
> ntc = 2,
> ntf = 2,
> tempi = 300.0,
> temp0 = 300.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 1000000, dt = 0.001,
> ntpr = 200, ntwx = 200, ntwr = 200
> /
>
>
> I would be grateful for any suggestions and/or for the pointing out of
> any glaring errors.
>
> Andrew Borgert
> Biophysical Sciences and Medical Physics
> University of Minnesota
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu