AMBER Archive (2008)

Subject: Re: AMBER: reg unstability of structure in md

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Dec 05 2008 - 05:41:40 CST

can you tell us what those 2 pictures are? the minimized and the MD?
is it the MD restart file, or the traj file? which file format options did
you use?
it's hard to help unless you tell us exactly what you have done.

On Thu, Dec 4, 2008 at 11:32 PM, balaji nagarajan
<balaji_sethu_at_hotmail.com>wrote:

> dear amber ,
>
> I am doing md for a junction structure .,
> its solved by xray diffraction and i am using that pdb for dynamics
> no ions were found in the structure and the pH was 7 during crystallization
> .,
> and no ligands present in it .,
> actually on doing minimization with truncated octahedralbox of water
> the water box and the dna are perfect .
> I did equlibration and md as in the tutorial for poly - AT
> but when i analysed the results as mentioned there .,
> i am getting the perfect plots
> but when i view the trajectories in vmd
> its giving a picture like ( i have attached ) this .
> what could be the reason for it
>
> thanks in advance
> balaji.,
>
> ------------------------------
> Date: Thu, 4 Dec 2008 06:28:12 -0500
> From: carlos.simmerling_at_gmail.com
> To: amber_at_scripps.edu
> Subject: Re: AMBER: reg unstability of structure in md
>
>
> we'll need more information, such as where the pdb file came from
> (experiment? what type, and how well defined is the structure? were any
> regions missing?), if there are experimental measures of stability, if ions
> are important, if pH is important, if there are any non-standard force
> fields involved (such as a ligand), and then we need to know more about the
> equilibration procedure that you used. finally, explain what you mean by "it
> went bad". what analysis did you do?
>
>
> On Wed, Dec 3, 2008 at 11:17 PM, balaji nagarajan <
> balaji_sethu_at_hotmail.com> wrote:
>
> dear amber ,
> I am a new user to amber ,
> I changed my pdb format and loaded in xleap its loaded ..,
> and i am sure my pdb is quite in a right form isn't it .,
> it gave a message in terminal like this ...
>
> dna1 = loadpdb "j0.pdb"
> Loading PDB file: ./j0.pdb
> total atoms in file: 808
> Leap added 448 missing atoms according to residue templates:
> 448 H / lone pairs
>
> I solvated the structure in water (TIP3P)
> by giving
>
> solvateoct model2 TIP3PBOX 8.0
>
>
> and i viewed the pdb its good
>
> but when i do the minimization and the procedure as given in poly-AT
> tutorial
> in explicit water for 120 ps ..
> my molecule is no more stable it went bad
> what could be the reason
> help me out to solve the problem
> thanks in advance .....
>
>
>
> ------------------------------
> Some big movies will hit the screen this Christmas. Catch all the previews
> and promos on MSN Entertainment Try it! <http://entertainment.in.msn.com/>
>
>
>
> ------------------------------
> It is a cricketing clash meant for the Gods! Be there when we track the
> T-20 Champions League this December Try it now!<http://sports.in.msn.com/>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu