AMBER Archive (2008)

Subject: Re: AMBER: Using antechamber without AMBER program

From: Surasak Chunsrivirot (fa833_at_MIT.EDU)
Date: Mon Feb 04 2008 - 18:38:07 CST

Hi,

Thank you very much. Your answer is very helpful. The reason that we
used CHARMM
and NAMD in our lab b/c we already have these sws. I know CHARMM to some
extent, and NAMD is very fast to run.

I heard that if parameters are not available for a molecule then Leap
might also
be needed, in addition to antechamber. Is that true? What is your
suggestion if
this happens.

Also, in the case of polymer (PGA for example) with infinite length (with
periodic boundary condition). Is antechamber able to automatically generate a
force field for this polymer? What should I do in this case? Build a force
field for a few monomers (5) maybe?

Thank you very much,
Surasak

Quoting Scott Brozell <sbrozell_at_scripps.edu>:

> Hi,
>
> On Mon, 4 Feb 2008, Surasak Chunsrivirot wrote:
>
>> I'm completely new to AMBER and our lab doesn't have AMBER program
>> yet. I want
>> to use AMBER force fields to do simulation of small molecules, using
>> CHARMM or
>> NAMD software.
>
> Ohhh my, why ? :)
>
>> I want to use antechamber to generate force fields for small
>> molecules such as drugs, solvents, excipients and wondering if I can
>> just use
>> antechamber program to do that.
>
> Yes.
>
>> Do I need to buy AMBER software if I want to
>> just generate force fields for small molecules? Your suggestions would be
>> greatly appreciated.
>
> No. For example, Amber score in DOCK uses antechamber:
> http://dock.compbio.ucsf.edu/DOCK_6/index.htm
> So does Chimera:
> http://www.cgl.ucsf.edu/chimera/
>
> Scott
>
>> If I need to buy AMBER, I'll try to convince my adviser to buy one.
>>
>> Thank you very much for your help.
>>
>> Sincerely,
>> Surasak (a PhD student)
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