From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Wed Mar 04 2009 - 13:05:22 CST
Carma is an excellent tool, and i don't understand why it is not so popular.
By the way, i had exactly the same problem and used psfgen for the
generation of new psf file.
I guess it would be nice to have one python (or tcl) script which
would call carma to handle dcd file, psfgen to create new psf file.
On Wed, Mar 4, 2009 at 12:51 PM, jose correa <corrjose_at_gmail.com> wrote:
> Thank you Nicholas and Adelman for your replay, I see that with "carma" is
> more easy. I have a question related to carma, i understant that the program
> generate a *dcd whitout water molecules and ions, but, to read this new *dcd
> are requiered a new its *psf?, or not?.
> Best wishes
> 2009/3/4 Nicholas M Glykos <glykos_at_mbg.duth.gr>
>> Hi Jose,
>> You can also use carma (I should add this to my .signature ;-) to both
>> remove waters and rotations/translations:
>> # carma -v -fit -atmid ALLID -segid A -segid B my.dcd my.psf
>> where the '-segid A -segid B ...' must match the SegIDs of the
>> macromolecular component.
>> Dr Nicholas M. Glykos, Department of Molecular
>> Biology and Genetics, Democritus University of Thrace,
>> University Campus, 68100 Alexandroupolis, Greece, Fax +302551030620
>> Tel ++302551030620 (77620), http://www.mbg.duth.gr/~glykos/
-- Roman Petrenko Physics Department University of Cincinnati
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