AMBER Archive (2009)

Subject: Re: [AMBER] using binary trajectories from NAMD in PTRAJ

From: karthik s (karthiks.mmc_at_gmail.com)
Date: Tue Jan 27 2009 - 00:49:13 CST

Thank you for the guidance. I generated parameters (top & crd) using LEaP in
AMBER. Thanks once again. Good day

On Mon, Jan 26, 2009 at 8:11 PM, Wei Huang <whuang_at_cct.lsu.edu> wrote:

> Hi Karthik,
>
> Yes, it is supported by ptraj to analyze dcd trajectory from NAMD. But you
> need a psf file in CHARMM format (notice: this is not the default psf file
> in NAMD) or an AMBER topology file to load up the trajectory.
>
> Best,
> Wei
>
> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf
> Of karthik s
> Sent: Monday, January 26, 2009 1:11 AM
> To: amber_at_ambermd.org
> Subject: [AMBER] using binary trajectories from NAMD in PTRAJ
>
> Dear Users,
> I simulated by protein system in NAMD. I wish to analyse the
> datas in PTRAJ module of AMBER. Is the format of binary trajectories (.dcd)
> from NAMD supported in AMBER. kindly help me in this regard.
> Thanks in advance.
>
> --
> karthik
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-- 
karthik
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