[gmx-users] covalent bond between ligand and protein
feenstra at chem.vu.nl
Wed Jan 14 13:58:03 CET 2004
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
> 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!
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
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