Re: [AMBER] Calculating Amber Force fields from Wikipedia

From: <>
Date: Tue, 16 Mar 2010 20:32:02 -0400

I'm confused now. If I take your suggestion and try to learn and duplicate sff.c
in my system...
...which remains to be seen if I can do it...then
I need to give it the prmtop info as input?

Here's what I have so far. My system can display a pdb file with visual bonds.
The system imports and parses up a pdb file. Make-Na generates the pdb file
from NAB.

Can make-na theoretically give me the prmtop info?

I would need some way of generating all the prmtop info manually or somehow
generate a prmtop file. I could contact James Stroud regarding this or hire someone
to do this task (the source code is available for make-na).

Is that about right?





-----Original Message-----
From: M. L. Dodson <>
To: AMBER Mailing List <>
Sent: Tue, Mar 16, 2010 2:58 pm
Subject: Re: [AMBER] Calculating Amber Force fields from Wikipedia

On Mar 16, 2010, at 4:30 PM, wrote:

> I can approach the problem similarly to folding at home. Keep in mind that I
am already using make-na by Stroud to generate the DNA.
> There are simple force field calculations supposedly somewhere in the nab
source files. Can someone tell me which of the 94 files contains the ff
algorithm. I'll attempt to understand the algorithm but I would be much more
comfortable with a corrected Amber equation if one exists that is good enough
for simulating just nucleic acids for k12 students.
> Thank you for the suggestions,
> Dan

Look in $AMBERHOME/src/sff/sff.c where the top of the file reads:

 * sff.c: simple force field: implement routines to read a "prmtop"
 * file from AMBER, and calculate the energy. Implements only
 * some of AMBER's functionality: bonds, angles, dihedrals, and
 * nonbonded interactions with a distance-dependent dielectric.
 * Does not (yet) include support for period systems.
 * Main interface is through routines "mme", "mme4", "mme_init_sff",
 * "mme_rattle" and "md".
 * Modifications to mme_init, mme, mme4 and md were added by
 * Russ Brown (

This should do what you want without a lot of bells and whistles.

You will be much happier using this approach than reinventing the wheel. Trust
me on this.

Let me correct one more misunderstanding, though. Paraphrasing Yoda: there is
no "good enough", there is "correct" and "not correct".

As you gain experience, you can learn the extra bells and whistles. Maybe you
will consider them to give you more than "good enough". Or not.

Good Luck,

Bud Dodson

> On Mar 15, 2010, at 8:45 PM, "M. L. Dodson" <>
>> I really had meant to quit responding to this topic, but what the heck.
>> On Mon, Mar 15, 2010 at 10:42:50PM -0400, wrote:
>>> It's really difficult to read other people's source code when
>>> converting something from one language to another especially porting
>>> to an object oriented language.
>>> It would be much easier though to just start from the correct
>>> equation --with the adjustment conditions if I can determine what
>>> they are.
>> I can almost guarantee that you are wrong on this point.
>>> Is the correct equation out there some where. I'm primarily
>>> interested in nucleic acids with (I'm learning) implied solvation?
>>> Should I start from the wikipedia entry and make all the adjustments
>>> and modfications to the code you mentioned. I don't think I'm going
>>> to be that successful digging through the source code unless it's
>>> superbly documented.
>>> What is your recommendation?
>> I'll let Ross speak for himself. I think my position is clear.
>>> Thanks for taking the time to enlighten me of all the problems and
>>> pitfalls.
>>> Dan
>>> -----Original Message-----
>>> From: Ross Walker <>
>>> To: 'AMBER Mailing List' <>
>>> Sent: Mon, Mar 15, 2010 7:16 pm
>>> Subject: RE: [AMBER] Calculating Amber Force fields from Wikipedia
>> Elide Ross's excellent dissection of the Wikipedia Amber FF entry.
>>> Good luck,
>>> Ross
>> Maybe you should be talking to the Folding.Home people (Use teh
>> Google!) They use the Amber FF with another simulation engine. My
>> understanding of the way they do it is to use leap to generate an
>> ordinary parameter-topology file for the structure to be simulated.
>> Then they have a special utility to convert the prmtop file to the
>> format used by their simulation engine. I am not aware of any other
>> simulation package that interprets the raw FF files directly (there
>> may be some, I just don't know of them). They all use the prmtop file
>> directly or as an intermediate representation of the simulation system
>> description. Leap is quite fast (especially for systems you are
>> likely to simulate, i.e., no ions or waters). It would be quite
>> feasible to run it on a server. If you want to use the prmtop as an
>> intermediate representation instead of interpreting the raw FF files,
>> see the nab source code for the readparm function.
>> 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
>> _______________________________________________
>> AMBER mailing list
> _______________________________________________
> AMBER mailing list

M. L. Dodson
Business email: activesitedynamics-at-comcast-dot-net
Personal email: mldodson-at-comcast-dot-net
Phone: eight_three_two-five_63-386_one
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Received on Tue Mar 16 2010 - 18:00:02 PDT
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