From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Thu Nov 15 2007 - 22:32:56 CST
Hi all,
I wasn't aware that one could get the Amber FF in a form that they could manipulate easily without owning Amber (this is probably because I have never used Amber); I know in my current work that the Amber FF in all its various flavors tends to give better optimized geometries than most of the other FF's out there, in some cases even better than SCC-DFTB (even Kollman's All-Atom FF is better!).
Of course, I'm aware that the CHARMM FF's are readily available in all their versions, and are easily manipulated (even I have done so on several occasions).
The reason I posted this was for this question as well as the person asking about how to read a NAMD dcd file into CHARMM. Myself, I would have just done my MD in CHARMM and analyzed it there, since he has CHARMM (obviously). Oh well...
Richard
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55414-2959
rwoodphd_at_yahoo.com
From: JC Gumbart <gumbart_at_ks.uiuc.edu>
To: Richard Wood <rwoodphd_at_yahoo.com>; namd-l_at_ks.uiuc.edu
Sent: Thursday, November 15, 2007 11:01:54 PM
Subject: RE: namd-l: howcan I use amber forcefield in NAMD?
RE: namd-l: howcan I use amber forcefield in NAMD?
<!--
_filtered {font-family:Tahoma;panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;margin-bottom:.0001pt;font-size:12.0pt;font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:blue;text-decoration:underline;}
p
{margin-right:0in;margin-left:0in;font-size:12.0pt;font-family:"Times New Roman";}
tt
{font-family:"Courier New";}
span.EmailStyle20
{font-family:Arial;color:navy;}
_filtered {margin:1.0in 1.25in 1.0in 1.25in;}
div.Section1
{}
-->
Technically, NAMD is forcefield
agnostic. Although in practice, most users probably use the Charmm
forcefield, I know of people that have used the Amber forcefield in NAMD which
may be better for some purposes (IĒve heard DNA is supposedly better with
Amber over Charmm, I donĒt know if itĒs still true anymore).
In that way, you would get the best of both the Amber FF and the scalability
and features of NAMD.
If the user is not looking for specific
Amber FF behavior though, I would agree with you. VMD along with Psfgen
are made for preparing Charmm FF-based files and therefore are probably the most
straightforward way to use NAMD as well.
From:
owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Richard Wood
Sent: Thursday, November 15, 2007
9:33 PM
To: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: howcan I use
amber forcefield in NAMD?
Hi all,
This might be a stupid question, but wouldn't one be best served to use force
fields with the programs that they were developed for; or alternatively,
prepare and create their systems so that they can be run in NAMD/CHARMM?
Richard
Richard L. Wood, Ph. D.
University of
Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717
Delaware St. SE
Minneapolis, MN 55414-2959
rwoodphd_at_yahoo.com
----- Original Message
----
From: Huy N. Ha <Huy.Ha_at_vcp.monash.edu.au>
To: mashaojie163 <mashao_jie_at_163.com>; namd-l_at_ks.uiuc.edu
Sent: Thursday, November 15, 2007 6:24:36 PM
Subject: RE: namd-l: howcan I use amber forcefield in NAMD?
The alternative would be to use Antechamber: http://amber.scripps.edu/antechamber/antechamber.html
which is distributed freely, and can generate the required top/crd amber
formats that you need as it contains tleap. The top file is the crucial file
you need (psf doesn't work for the amber force field), as for the crd file, it
will end up generating a coord(pdb) file after the minimization run anyway.
Also, if I remember correctly, NAB also contains tleap http://www.scripps.edu/mb/case/casegr-sh-3.2.html
and might suit your purpose?
Mr. Huy Ha
B. Med. Chem. Honours Student
Dept. of Medicinal Chemistry
Victorian College of Pharmacy
Monash University
381 Royal Parade,
Parkville, VIC, 3052
Phone No: 99039711
Ext: #39711
Email: Huy.Ha[at]vcp.monash.edu.au
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu on behalf of
mashaojie163
Sent: Thu 11/15/2007 11:23 PM
To: Irene Newhouse; namd-l
Subject: Re: namd-l: howcan I use amber
forcefield in NAMD?
Dear Irene Newhouse:
Thank you for your quick
response. I don not have amber. I find there are two file in the
directory amber9.ffparms\dat\amberff_in_charmm\ cornell_all.prm and
cornell_all.rtf. It seems that the two file is charmm format of amber field.
Can I use it directly? Can I use cornell_all.rtf to create
psf file and then use cornell_all.prm as parameter file to conduct my
calculation?
----- Original Message -----
From: Irene Newhouse
To: mashaojie163 ; namd-l_at_ks.uiuc.edu
Sent: Thursday, November 15, 2007 2:51 PM
Subject: RE: namd-l: howcan I use amber
forcefield in NAMD?
When you use the AMBER forcefield with
NAMD, you will not have a psf file. That is CHARMM-style. You will have a
prmtop file and an inpcrd file. The easiest way to generate these is by
using tleap, which is a utility that comes with AMBER9, and only with AMBER9.
The good news is that the academic price for AMBER is very reasonable.
Instructions for using tleap can be found in the AMBER documentation. You
create these files from a pdb input file. You can use xleap, a GUI version of
tleap, to build proteins, too, but I've never tried that.
The parameter files come with AMBER. You
want to use ff99SB, which better simulates alpha-helical sections of protein
than ff99. [That will make sense once you start looking at how to use
tleap].
VMD can display prmtop & inpcrd files
in a way similar to pdb/psf combinations. When you animate a dcd file computed
with AMBER input with NAMD, you use the prmtop file in the same way as a psf
file.
Once you get hold of AMBER, write me
off-line if you run into trouble & I'll try to help you out.
Irene Newhouse
> From: mashao_jie_at_163.com
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: howcan I use amber
forcefield in NAMD?
> Date: Thu, 15 Nov 2007 11:58:39 +0800
>
> Dear Sir:
> How can I use amber force field to
calculate protein.
> I think that I should do this
according to the following 3 steps.
>
> 1) I should generate a psf file and a
coord file. Which top file should be used to gererate the psf file? Where can I
download the topfile? What type is the coord file?? Is PDB OK??
>
> 2) I should have a amber parameter
file. Which parameter file should I choose? Where can I download the parameter
file??
>
> 3) I should modify the configure file
acoording
> http://www.ks.uiuc.edu/Research/namd/2.6/ug/node15.html.
> then I run NAMD.
>
>
> So, there are so many questions before
I excute the 3rd step. Please help me and answer the questions in detail! Thank
you very much??
> Best Regards
>
**************************************************
> Shaojie Ma
>
Institute of Nano Science
>
Nanjing University
of Aeronautics and Astronautics
> mashaojie_at_nuaa.edu.cn
> Nanjing
210016, China
>
**************************************************
>
------------------------------------------------------------------------------
Peek-a-boo FREE Tricks & Treats for
You! Get 'em!
Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try
it now.
____________________________________________________________________________________
Be a better sports nut! Let your teams follow you
with Yahoo Mobile. Try it now. http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:33 CST