[Chimera-users] NAMD trajectory and AMBER topology

Eric Pettersen pett at cgl.ucsf.edu
Tue Mar 2 14:28:25 PST 2010

Hi Francesco,
	Unfortunately Chimera doesn't support the prmtop/DCD combo.  The only  
possibility I can find is to convert your prmtop to a psf in VMD as  
described in this mail (option "a"):


But at that point you are already using VMD and I don't see why you  
wouldn't just go ahead and visualize your trajectory using that  
instead of relying on the shaky prmtop->psf conversion.

	I will open a feature-request ticket in our Trac database for  
allowing "mix and match" of topology/coordinate formats, with you on  
the recipient list.

                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Mar 2, 2010, at 3:43 AM, Francesco Musiani wrote:

> Hi all,
> I would like to visualize in Chimera a trajectory obtained with the  
> program NAMD,
> but I have a .prmtop topology file generated using AMBER instead of  
> a .psf topology file.
> I have these files beacuse in NAMD is possible to use AMBER format  
> topology.
> Is it possible to implement an additional feature in Chimera which  
> allows to visualize
> NAMD trajectory using AMBER topology?
> Thanks in advance,
> Francesco
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