RE: AMBER: reg unstability of structure in md

From: balaji nagarajan <>
Date: Fri, 5 Dec 2008 10:02:21 +0530

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

Date: Thu, 4 Dec 2008 06:28:12 -0500
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 <> 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!

Register once and play all contests. Increase your scores with bonus credits for logging in daily on MSN.

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

(image/png attachment: md_1crdwithwaterbox.png)

(image/png attachment: molecule.png)

Received on Fri Dec 05 2008 - 18:48:46 PST
Custom Search