From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Tue May 05 2009 - 10:44:55 CDT
Hi Jorgen,
If you are running a simulation using the Amber force field, you
should not be supplying a psf file. All of the information should be
contained in the coordinate (ambercoor) and parameter (parmfile) files
that you supply from setting up the system using AmberTools.
Josh
PS - Please make sure you reply to the list as well so that others can
benefit from the questions/answers.
On May 5, 2009, at 2:59 AM, Jorgen Simonsen wrote:
> Hi
>
> Thanks for the answer - I am a little bit puzzled with generating
> the psf - the charge between the topology file from the charmm are
> different from amber charge so how does NAMD handle this?
>
> Thanks in advance
>
> Best
>
> J
>
>
>
>
>
> On Mon, May 4, 2009 at 5:41 PM, Joshua Adelman
> <jadelman_at_berkeley.edu> wrote:
> Hi Jorgen,
>
>
> On May 4, 2009, at 1:22 AM, Jorgen Simonsen wrote:
>
> Hi all,
>
> I have a simulation where I would like to use amber parameters
> instead of charmm. I have looked in the tutorial and it seems that
> it is possible to run.
>
> 1. Is it possible to freeze atoms during either minimization or MD
> simulation and where to add the constraint - normally I would use
> the B-column in the pdb file but it seems that is not included in
> the amber or is it?
>
>
> After you build your system in AmberTools and get the prmtop and
> inpcrd (topology/ff and coordinates, respectively), I am pretty sure
> you can load one of those two files into VMD (I did this recently,
> but I forget which one I used, but I know one of them works). From
> there you just go about building the fixed/restraint pdb files as
> you normally would using the B-column. Just writepdb as usual and
> stick it in the config file.
>
>
>
> 2. As I would like to run a NPT simulation is it possible to use
> the langevin pistion for both the temperature as well as the pressure?
>
>
> You would want to use both the Langevin Piston for your barostat and
> the Langevin dynamics for your thermostat. You cannot control both
> temperature and pressure with the langevin piston alone, as far as I
> can tell from reading the user's guide.
>
> Josh
>
>
> Any help - appreciated thanks in advance
>
> Best
> J
>
> ------------------------------------------------------------------------------------------------------
> Joshua L. Adelman
> Biophysics Graduate Group Lab: 510.643.2159
> 218 Wellman Hall Fax: 510.642.7428
> University of California, Berkeley http://nature.berkeley.edu/~jadelman
> Berkeley, CA 94720 USA jadelman_at_berkeley.edu
> ------------------------------------------------------------------------------------------------------
>
>
>
>
------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
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