[gmx-users] merge option in pdb2gmx

[Anton Feenstra]

David van der Spoel wrote:

> On Sun, 8 May 2005, Valentin Gogonea wrote:
> 
> 
>>GMX users,
>>
>>I am trying to make a bridge between two peptide chains using the 
>>specbond.dat file. It works only if the "merge" option in the pdb2gmx 
>>is used, but in this case pdb2gmx creates a bond between the two 
>>peptide chains which eliminates two of the chain termini (one from each 
>>peptide). Is there a way to avoid this elimination of termini?
> 
> yes, give the chains a different chain label.

It would be nice if pdb2gmx understood the 'TER' field in a .pdb file...
(At least, that is less work to add than chain id's.)

-- 
Groetjes,

Anton

* NOTE: New Phone & Fax numbers (below) *

  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
|_____________|_______________________________________________________|