[gmx-users] covalent bond between ligand and protein

[Anton Feenstra]

David van der Spoel wrote:

> On Tue, 2004-01-13 at 17:09, muthu12 at cox.net wrote:
> 
>>Is there any example for specbond.dat How grommp will read that file
>>thank you
> 
> share/top/specbond.dat
> 
> it's read by pdb2gmx

You should know that distances in the specbond.dat file are the 'requested'
distances and bonds are only created if the deviate less than 10% (IIRC)
from that value.

There is an alternative method by re-numbering your ligand so it can be
placed 'after' the protein in the topology file. Bonds etc. can then be
added manually. I've posted a few scripts to facilitate this process,
both to the list and to the Contributions page. Have a search and a look!


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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