AMBER Archive (2006)

Subject: Re: AMBER: Programes to calculate ligand RMSD

From: Carlos Simmerling (
Date: Fri Jun 02 2006 - 06:45:17 CDT

ptraj is what most of us use- is there a reason
it won't work? there is plenty of information in
the manual and the tutorials on how to use it.

nag raj wrote:

>Dear amber users,
> I have taken few conformations of a
>ligand(same ligand)from Protein Data Bank. I want to
>calculate RMSD of these conformations. Could any one
>tell me, any softwares, databases or servers are
>available to calculate RMSD of liagnds.
> Thanks in advance.
> bye
> nagaraju
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