Re: howcan I use amber forcefield in NAMD?

From: Richard Wood (
Date: Thu Nov 15 2007 - 21:33:00 CST

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 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 <>
To: mashaojie163 <>;
Sent: Thursday, November 15, 2007 6:24:36 PM
Subject: RE: namd-l: howcan I use amber forcefield in NAMD?

RE: namd-l: howcan I use amber forcefield in NAMD?


The alternative would be to use Antechamber: 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 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]

-----Original Message-----

From: 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 ;

  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:

> To:

> 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


> 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


> Nanjing 210016, China

> **************************************************



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