AMBER Archive (2006)

Subject: Re: AMBER: change mdcrd file to pdb file

From: Fabian Alejandro Rodriguez (far217_at_nyu.edu)
Date: Sun Sep 17 2006 - 11:04:22 CDT

here you can have an example:
trajin ../../mBdnaVac300Kprod800psC2.traj.gz 3335 3335
#trajout lowest_rms.crd restart nobox
trajout lowest_energy.pdb pdb nobox

but, did you look at the tutorials by Ross Walker? you can basically
find all the answer to your questions there.
http://www.rosswalker.co.uk/tutorials/amber_workshop/

> Somebody tells me Ptraj can be used to convert mdcrd
> file to a series of RMSD file. But I have not tried
> yet. If you know the exact command, please let me
> know.
>
trajin ../../mBdnaVac300Kprod800psC2.traj.gz
reference lowest_energy.pdb.3335
#rms reference out iBdnaVac300Kprod800psC3.rmsfit @P,O3',O5',C3',C4',C5'
time 0.20
rms reference mass out mBdnaVac300Kprod800psC2.rmsfit time 0.20
#pucker p1 :1_at_C1' :1_at_C2' :1_at_C3' :1_at_C4' :1_at_O4' out p1.dat cremer offset
-90.0

good luck.
fabian.

> Best regards.
>
> Fenghui Fan
>
> --- Jianhui <tianj_at_rpi.edu> wrote:
>
> > Hello Fenghui,
> >
> > Why don't you want to change mdcrd file to pdb file?
> > What I know is you can change rst file to pdb file
> > by ambpdb:
> > $AMBERHOME/exe/ambpdb -p prmtop < rst > pdb
> >
> > Best regards,
> >
> > ======= At 2006-09-17, 01:02:54 you wrote: =======
> >
> > >Will you please tell me the exact command to
> > convert
> > >mdcrd file to pdb file by ambpdb?
> > >
> > >Best regards.
> > >
> > >Fenghui Fan
> > >
> > >__________________________________________________
> > >Do You Yahoo!?
> > >Tired of spam? Yahoo! Mail has the best spam
> > protection around
> > >http://mail.yahoo.com
> >
> >-----------------------------------------------------------------------
> > >The AMBER Mail Reflector
> > >To post, send mail to amber_at_scripps.edu
> > >To unsubscribe, send "unsubscribe amber" to
> > majordomo_at_scripps.edu
> > >
> > >
> >
> > = = = = = = = = = = = = = = = = = = = =
> >
> > Jianhui
> > tianj_at_rpi.edu
> > 2006-09-17
> >
> >
> >
> >
> -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to
> > majordomo_at_scripps.edu
> >
>
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam? Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

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