[gmx-users] pdb2gmx and terminal proline

[Anton Feenstra]

David van der Spoel wrote:

> On Wed, 2003-11-26 at 08:21, Graham E Jackson wrote:
> 
>>Dear All,
>>I have used pdb2gmx to convert a pdb file of a cyclic SS peptide built
>>in INSIGHT.  The peptide has an N-terminal proline. The command line I
[...]
> You mean after energy minimization?
> Can you send me the structure before and after EM?


I have seen *terribly* distorted conformations of sidechains in
structures generated by Insight for aromatics, but that might extend
to prolines in some cases as well.

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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