AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Dec 04 2008 - 05:28:12 CST

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 .....
>
>
>
> ------------------------------
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