AMBER Archive (2003)

Subject: ALAscan of Proline

From: Martin Lepsik (lepsik_at_marilyn.uochb.cas.cz)
Date: Mon Jul 07 2003 - 16:14:09 CDT

Hello AMBER community,
I have run into problems with the MM-PBSA module when ALA-scanning
Proline residues. When creating traj files, the program strips
CG,HGs,CD, and HDs from Prolines correctly but doesn't add the nitrogen
H atom resulting in a bad crd file.

Is there a way to tell the ALAscanning routine there's a proline which
needs to be given a proton? Or a workaround?

Thanks in advance.

Best regards,

Martin Lepsik