On Wed, Mar 05, 2014, DEBOSTUTI GHOSHDASTIDAR wrote:
>
> I went a step back and visualized the leap
> generated pdb and it was a perfect A-DNA. However, when I loaded the leap
> generated crd file on the leap generated topology file, the structure
> looked severely distorted.
This should not happen. The coordinates leap puts into the pdb file
should be the same as those it puts into the crd file. (If you are using
solvateBox, add "set default nocenter on" at the top of your leap.in
file.)
It sounds like the problem is at the LEaP step: if you start with a severely
distorted structure, you are indeed likely to have problems. You need to try
to figure out what is going wrong at this early step.
> I guess the A-DNA structure was disturbed during minimization.
This is confusing: above you said you were seeing distortions with the
"leap generated crd file on the leap generated topology file". If so, bad
things must have happened before any minimzation.
>
> For re-confirming, I visulalized the leap generated crd and topology files
> given in the Amber tutorials Section B1 (Simulation of DNA) and even that
> structure was distorted. Where am I going wrong?
What visualization program are you using? Exactly what commands are you
executing? The problem may be in how you are using the visualization program,
but we can't help there, since we don't even know which program you are using.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 05 2014 - 05:30:05 PST
