[gmx-users] combine mutiple PBDs

[Justin Lemkul]

On 3/29/13 6:12 AM, Zalikha Ibrahim wrote:
> Hi to all GMX users,
>
> I would like to ask. Can we merge several PDB files (taken from PDB) into
> an .xtc?
> I tried using tjcat, but received the following response.
>
>> Fatal error:
>
> Different numbers of atoms (4829/5145) in files
>
> Is there any way to make trjcat ignore the difference in atoms no, or
> perhaps any other suggestion to merge them?

The integrity of an .xtc file relies on uniformity of the frames, so no, there 
is no way to bypass this requirement.  What purpose do you have for merging 
these files?  You might be able to create a multi-frame .pdb file by simply 
using the cat command, but likely many programs will fail for the same reason. 
Once a frame is interpreted, it is generally assumed that the remaining frames 
will have the same contents, just different coordinates.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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