Re: AMBER: Hydrogen bonding question

From: Carlos Simmerling <>
Date: Tue, 15 Mar 2005 10:48:41 -0500

these start to be questions about science, not ust using Amber.
you need to make sure that your sampling is complete, you should
look carefully at any differences between the force field parameters
that you used and those used in the article that you mentioned.
I would expect that antechamber would only be a good starting place for
PNA parameters- you'll probably need to adjust them much as the
protein parameters have been adjusted over the years. You should
read articles about how this has been done, since it is way beyond the
scope of simple email help lists. I think that in cases like this you
want to have good experimental data to validate your parameters
before studying something where the structural details are not known.
that's my opinion, anyway... good luck!

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:
=================================================================== wrote:

>>Dear Amber Community,
>>I am trying to simulate a single strand of an oligonucleotide. This
>>results in a the strand folding onto itself in implicit solvent.
>>Then I tried to place it in explicit solvent and equilibrate the pressure
>>to 1 bar. Then I removed the restraints from the molecule and let it
>>move. Agin, this resulted in the strand folding onto itself.
>do you have reason to think that this is not correct?
>Yes, I am trying to simulate a 12-mer PNA. Other simulations with PNA's,
>done by other people in the literature, seem to indicate that PNA's are
>not prone to hydrogen-bond onto itself. (Example of this can be seen
>here: JACS, 2001, 123, 7414-7422, Srikanta Sen, Lennart Nilsson) So based
>on this, I thought that PNA's are not likely to fold onto itself and
>hydrogen bond with nucleotides on the other end of the strand. If this is
>not the case, is this just an arteract of the program used in the paper
>mentioned above? And if this i the case, how can I be more certain of
>what to use and what is "more accurate"?
>I made the PNA residues and then calculated the charges using antechamber
>and the bcc method.
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Received on Tue Mar 15 2005 - 15:53:00 PST
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