Re: [AMBER] regarding forcefield for rna

From: Asfa Ali <asfa.iisc.gmail.com>
Date: Fri, 11 Jun 2010 16:39:24 +0530

Hi,

Thanks for all your suggestions. I tried the following with pdb id: 2kbp

tleap -s -f leaprc.ff99bsc0
loadoff RNA_CI.lib
dna = loadpdb ....
...

I carried out a production run for 6ns after all the haeting and
equilibration runs and again at the beginning of the run, the two strands
split open as shown in the attachment.

As suggested, I'll try by incorporating central Na+ ions.

Asfa.


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2kbp_md2_pdb1.png
(image/png attachment: 2kbp_md2_pdb1.png)

Received on Fri Jun 11 2010 - 04:30:05 PDT
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