[gmx-users] doubts on g_confrms output

[Mark Abraham]

On 12/02/2011 7:07 PM, Tsjerk Wassenaar wrote:
>
> Hi,
>
> 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.

Mark


> Cheers,
>
> Tsjerk
>
>> 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.
>>
>> Mark
>>
>> > ________________________________ > From: Mark Abraham 
>> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> > To: 
>> Discussion...
>>
>>
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