[gmx-users] problem with specbonds

[Anton Feenstra]

David wrote:
> On Thu, 2003-05-22 at 18:47, quantix1 at gmx.de wrote:
> 
>>Hi all,
>>
>>I'am trying perform a cyclization using pdb2gmx, so I wouldn't have to edit
>>the topology
>>file by hand. I'd like to connect the side chain of ornithine to the
>>C-terminus of the last
>>amino acid. The line I have added to specbonds.dat looks like this:
>>
>>ORN     NE      1       ARG     C       1       0.2     ORN     ARG
> 
>                                                   ~~~
>   change this to                                 0.14

The point here is that the distance in specbonds.dat is not an upper
limit, but a 'target distance'. The bond will only be created if the
actual distance is within 10% of the target!

This can be a real pain if you want to start simulations from, e.g.,
multiple X-ray structures in which the distance happens to differ more
than 20%; in that case no single distance in specbonds.dat allows all
X-ray files to be processed automatically by pdb2gmx. I'd suggest we
should either change it to an upper limit, or to specify an upper and
lower boundary.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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