Or you could just use leap.
On Mar 16, 2010, at 8:32 PM, whimsica.aol.com wrote:
>
> 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.
>
> http://structure.usc.edu/make-na/server.html
>
> 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?
>
> Dan
>
>
>
>
>
>
>
>
> -----Original Message-----
> From: M. L. Dodson <activesitedynamics.comcast.net>
> To: AMBER Mailing List <amber.ambermd.org>
> 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, Whimsica.aol.com 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 (russ.brown.sun.com).
> */
>
> 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" <activesitedynamics.comcast.net
>> >
> wrote:
>>
>>> I really had meant to quit responding to this topic, but what the
>>> heck.
>>>
>>> On Mon, Mar 15, 2010 at 10:42:50PM -0400, whimsica.aol.com 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 <ross.rosswalker.co.uk>
>>>> To: 'AMBER Mailing List' <amber.ambermd.org>
>>>> 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.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> 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
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 16 2010 - 18:30:04 PDT
