Re: [AMBER] difference in output from bnda and fd_helix functions

From: Igor Sizov <>
Date: Thu, 25 Mar 2010 15:07:07 -0400

The problem actually is that when I am trying to follow the tutorial for
building DNA and to hold the solute fixed (section 5.1.3) I need to point
out how many atoms will be fixed by using the command RES in the GROUP
input. In the case of two chains in a pdb file the number of residues is
only half of the actual number of residues in the file. So, itís just
impossible to make all atoms fixed. In the case of one chain in a pdb file
this is not a problem.

Thank you,


On Thu, Mar 25, 2010 at 1:26 PM, case <> wrote:

> On Wed, Mar 24, 2010, Igor Sizov wrote:
> >
> > I created two pdb files for the same DNA sequence with bdna and fd_helix
> > functions:
> >
> > These files are almost the same but bdna created two chains in the
> ChainID
> > column. Is this difference critical? Or I can use both files equally.
> Should be irrelevant for most applications.....dac
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Received on Thu Mar 25 2010 - 12:30:02 PDT
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