AMBER Archive (2008)
Subject: Re: AMBER: reg unstability of structure in md
From: N.R. Jena (nrjena_at_gmail.com)
Date: Fri Dec 05 2008 - 00:48:50 CST
You might need to check wheher you have selected right topology and
On Fri, Dec 5, 2008 at 12:32 PM, balaji nagarajan
> 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
> 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>
> 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
> 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
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> Champions League this December Try it now!
Nihar Ranjan Jena
C/O: Prof. Ying-Chieh Sun
Department of Chemistry, National Taiwan Normal University, 88,
TingChow Road, Section 4, Taipei 116, Taiwan
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