[gmx-users] pdb2gmx and terminal proline
feenstra at chem.vu.nl
Thu Nov 27 10:40:08 CET 2003
David van der Spoel wrote:
> On Wed, 2003-11-26 at 08:21, Graham E Jackson wrote:
>>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.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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