AMBER Archive (2004)

Subject: Re: AMBER: converting from NAMD trajectory format

From: Thomas E. Cheatham, III (
Date: Wed Dec 08 2004 - 18:53:50 CST

> I'm interested in using ptraj in amber, but my trajectory file
> is from NAMD (a .dcd file). Does anyone know how I may convert
> my NAMD trajectory file to the proper AMBER trajectory file
> format?

If you have the PSF file, ptraj can read psf/dcd combos, at least
normally... Try it out and if it doesn't work, let me know and we can try
to fix it, but in general I've run the program with CHARMM produced files
without trouble.

(There is no easy way to convert PSF->prmtop at present; while you can
convert the DCD, you will still need a 1-to-1 corresponding prmtop from
AMBER for it)

Good luck.

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
| (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418

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