AMBER Archive (2004)

Subject: Re: AMBER: Trajectory file conversion between Amber & Charmm

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Sep 20 2004 - 12:59:41 CDT

this is confusing - if you don't have charmm parm/top files, how did you
generate the charmm trajectories?

CK Sim wrote:

> To do analysis on Charmm trajectories, I need the Charmm topology and
> parameter files. I already have the these files in Amber format,
> therefore the question lies in how to convert these files into Charmm
> format. Does anyone have a clue?
>
> Choon
>
> */Ross Walker <ross_at_rosswalker.co.uk>/* wrote:
>
> Ptraj that ships with Amber 8 should be able to do this. Although
> I haven't verified that it works in all cases, periodic vs
> non-periodic boundaries etc.
>
> Look at page 196 of the Amber 8 manual.
>
> Specifically you would want the following input file for ptraj
> (for amber to charmm):
>
> trajin inputtrajectory.traj.gz
> trajout outputtrajectory charmm
>
> Or for charmm to amber:
>
> trajin inputtrajectory.dcd
> trajout outputtrajectory trajectory
>
> Note, in both cases you will need a valid amber prmtop file for
> your molecule.
>
> I hope this helps.
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
>
>
> ------------------------------------------------------------------------
> *From:* owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] *On Behalf Of *CK Sim
> *Sent:* 24 August 2004 13:42
> *To:* amber_at_scripps.edu
> *Subject:* AMBER: Trajectory file conversion between Amber &
> Charmm
>
> Greetings, I am a user of both Amber and Charmm. My research
> work involves finding the trajectories of RNA molecules. In
> Amber, this information is stored in a file called *.traj
> which I compressed in a file format *.traj.gz. In Charmm, this
> information is stored in *.dcd. I use both Amber and Charmm
> frequently. Sometimes, the same input data is run on both
> Amber and Charmm because they give different information of
> interest. However, this takes up a lot of computer resources
> and processing power.
>
> My question, therefore, is that whether there exists a way to
> convert .traj file formats interchangably from Amber to .dcd
> file formats in Charmm and vice versa. Hope you can help!
>
>
>
> ------------------------------------------------------------------------
> Do you Yahoo!?
> Yahoo! Mail is new and improved - Check it out!
> <http://us.rd.yahoo.com/mail_us/taglines/new/*http://promotions.yahoo.com/new_mail>
>
> ------------------------------------------------------------------------
> Do you Yahoo!?
> vote.yahoo.com <http://vote.yahoo.com> - Register online to vote today!

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu