AMBER Archive (2005)

Subject: AMBER: improper torsion parameters

From: Simon Whitehead (SJW084_at_bham.ac.uk)
Date: Tue Sep 13 2005 - 12:23:13 CDT

Dear amber users,
 
Following the generation of the prmtop and inpcrd files using leap i noticed, on reading of the leap.log, that there were 2 missing sp2 improper torsion angle parameters;
 
C*-CN-CB-CA
NA-CA-CN-CB
 
 Do these relate to out-of-plane bending? When i examined my pdb file i found that these belonged to the lone tryptophan residue in my protein so i presume they relate to the ring itself. I am using the ff03 forcefield and was wondering if someone could provide me some assistance?
 
Kind Regards
 
Simon Whitehead
P.h.D student
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