On Thu, 2014-03-20 at 16:32 +0800, Neha Gandhi wrote:
> Dear List,
>
> I am using following cpptraj script:
> trajin X.mdcrd
> trajin Y.mdcrd
> strip :WAT
> strip :Na+
> trajout prod.crd (or trajout prod.netcdf netcdf)
>
> The final trajectory in .netcdf format can be visualized properly in UCSF
> Chimera orVMD but the trajectory prod.crd shows strange bonds upon
> visualization. If I use *trajout prod.crd nobox*, there are no issues with
> visualization.
>
> Am I missing out something? Is there alternative method to output the
> trajectory in .crd format?
Programs often need to be told whether or not box information is present
in the trajectory. For VMD, you need to select "Amber Coordinates with
box" when box info is present in your mdcrd.
There is probably something similar in Chimera.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Mar 20 2014 - 05:00:06 PDT
