AMBER Archive (2008)

Subject: Re: AMBER: concerning force fields

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jun 27 2008 - 07:34:21 CDT

I think your request is still much too vague to ask on an email list.
please try specific questions based on what you did not understand
from the tutorial, or based on what the tutorials taught you ask
specific questions about how things are not working for your
molecule. Others may be able to help you, but I find a question
like "how do I develop force fields" just too broad to answer in
an email. people have written many papers and review articles
about this, so that's probably a better resource for general learning.
check existing alkane parameter sets and decide why and how you
want yours to differ based on reading the articles about the results.
you might also try something like antechamber, but I think it's best
to start with established parameters until you have a lot of experience
and know the limitations of existing data and some ideas how to
improve it.

sorry I can't be more help- maybe others can.
carlos

2008/6/27 Adrien Delmont <adriendelmont_at_yahoo.com>:
> Dear Simmerling,
>
> In fact, I just done some of the tutorials . And I'm still working on them
> and also looking over them. But I need to know some extra information about
> this issue and need some expert advice and suggestions. You mentioned
> about an important point that 'How you proceed can depend on what type of
> molecules you want to simulate ' . So according to my study what must I do
> to create different force fields. In this sense, I'm waiting for your
> contributions.
>
> Many thanks in advance.
>
> Best regards,
>
> Adrien
>
> ----- Original Message ----
> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> To: amber_at_scripps.edu
> Sent: Thursday, June 26, 2008 10:25:04 PM
> Subject: Re: AMBER: concerning force fields
>
> Hi Adrien,
> have you worked through the tutorials on the web site?
> They can be helpful- if not, let us know that you're looking for
> more detail or so on.
> carlos
>
> 2008/6/26 Adrien Delmont <adriendelmont_at_yahoo.com>:
>> Dear Simmerling,
>>
>> I want to say sorry because I completely forgot to mention my structure I
>> study on. I'm interested in n-alkanes and evaluating thermophysical and
>> structural properties of n- alkanes and binary mixtures of n-alkanes.
>> What are the main steps and levels of creating a different force
>> field?
>> What must I do step by step ? In these conditions I 'm waiting for your
>> help and also all Amber user's help.
>>
>> Many thanks in advance.
>>
>> Best regards,
>>
>> Adrien
>>
>> ----- Original Message ----
>> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
>> To: amber_at_scripps.edu
>> Sent: Thursday, June 26, 2008 7:16:48 PM
>> Subject: Re: AMBER: concerning force fields
>>
>> have you checked the tutorials? There is a nice one there on force field
>> development for non-standard residues. I think your question is a bit too
>> open to get much help by email- are you interested in small molecule
>> force fields, unusual amino acids, sugars, etc? How you proceed can
>> depend on what type of molecules you want to simulate.
>>
>>
>> On Thu, Jun 26, 2008 at 11:14 AM, Adrien Delmont
>> <adriendelmont_at_yahoo.com> wrote:
>>> Dear All,
>>>
>>>
>>>
>>> I'm using Amber 9 v. My goal is to create different force fields that
>>> Amber
>>> does not provide for my molecular structure. I want to ask you some
>>> questions about creating different force fields in Amber . What are the
>>> main steps and levels of creating a different force field? What must I
>>> do
>>> step by step ? Could you give me some information about this ? Please
>>> help
>>> me to understand the basics of this procedure.
>>>
>>> Many thanks in advance.
>>>
>>> Best regards,
>>>
>>> Adrien
>>>
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>
>
>
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
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Stony Brook University E-mail: carlos.simmerling_at_gmail.com
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