From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Nov 15 2007 - 22:01:54 CST
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 (I've heard
DNA is supposedly better with Amber over Charmm, I don't know if it's 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
----- 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
> **************************************************
>
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