Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?

From: <>
Date: Mon, 15 Mar 2010 21:52:39 -0400

 You're right that they could run it on the server. It would probably work but it would
also tie up the server if it's a lot of calculations. A client only solution would be better.

I don't know if this will work at all. But I'm curious and skeptical just like you are. But I also don't
think that it will take that long to code up. I've already got the dna molecule in the system and
am using make-Na to get the molecule.

The good thing is that it doesn't have to be that accurate to illustrate what I would like
to illustrate so it's worth a try. Plus I get to learn about molecular dynamics.





-----Original Message-----
From: M. L. Dodson <>
To: AMBER Mailing List <>
Sent: Mon, Mar 15, 2010 6:31 pm
Subject: Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?

On Mon, Mar 15, 2010 at 08:10:26PM -0400, wrote:
> Thank you very much for the additional information.
> I am using NAB but in the form of make-na by james stroud to get the
> molecules.
> Amber Tools will not work because it will be running on the web.

I don't see that as a problem. You have to run the application on
some computer functioning as a server. Why can't you run the nab
program out of a "cgi script" (do they still call them that? I
haven't written for the web in a VERY long time)? I'm pretty sure
something like that is what make-na does.

> Won't amber forces alone be realistic enough to handle hyrogen
> bonding between base pairs in dna strands. The only purpose right
> now is to show hydrogen bonds between bases breaking and forming
> between dna strands. Will the amber force fields alone be
> sufficiently accurate for this purpose?
> Thanks,
> Dan

I'm not worried about the ability to simulate what you want. Yes, of
course it can do what you want. What does worry me (and bugs me a
little, to be frank) is the idea that you can code up some random
equation from Wikipedia, and expect it to (1) be correct and (2) be
made available to users in a reasonable period of time. CORRECT
molecular dynamics s/w is substantially more subtle than that, as is
the knowledge to use that software to produce meaningful results.
Those are the points you are missing. IMO.

The C source code to do everything you want is available, and I have
furnished a pointer to it. The various leap programs embody all the
methods to read and interpret AMBER parameter and topology files given
an input structure file. Nab embodies the methods used to carry out
simulations (and to do many other things) given the output of leap and
initial atomic coordinates. As they say: "Use the source, Luke!".

Good luck,

Bud Dodson
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email: mldodson-at-comcast-dot-net
Phone:  eight_three_two-56_three-386_one
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Received on Mon Mar 15 2010 - 19:00:05 PDT
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