[gmx-users] doubts on g_confrms output
Mark.Abraham at anu.edu.au
Sat Feb 12 10:03:18 CET 2011
On 12/02/2011 7:07 PM, Tsjerk Wassenaar wrote:
> The error message says the number of atoms in the first frame is not
> what was expected. That indicates the reference structure didn't
> match, which suggests the pdb file with the fitted structures wasn't
> used as reference. Solution: give the fitted structures both as
> reference (-s) and as trajectory (-f) with trjconv.
From the contents of the .pdb file the OP posted, I think the different
number of atoms in each PDB model is a feature/bug of g_confrms. The
documentation doesn't make clear what the output should be, however.
>> On Feb 12, 2011 2:19 AM, "Mark Abraham" <Mark.Abraham at anu.edu.au
>> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>> On 12/02/2011 3:45 AM, Kwee Hong wrote: > > Hi Mark, > > I tried but
>> with this error: > > Fatal erro...
>> OK. I don't know why two frames with different numbers of atoms are
>> written. Maybe g_confrms -one is useful. Or you can chop apart the
>> PDB by hand in a text editor.
>> > ________________________________ > From: Mark Abraham
>> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> > To:
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