AMBER Archive (2002)

Subject: dummy atoms.

From: Yongjun Jiang (yjjiang_at_mail.shcnc.ac.cn)
Date: Sat Apr 20 2002 - 22:20:44 CDT

Dear all,

I am a new user of Amber. A lysine molecule was mutated to a dummy
molecule, and I organized the out file as :

MASS
....

BOND
....

ANGLE
.....

DIHE
X-DT-DT-X 9 1.40 0.0 3.0
....

WHen I used "saveamberparmpert " command, the message displayed :

****Proper torsion paramter is missing****
  atom names : HB3-CB-CG-HG3
  atom types : HC-CT-CT-HC =pert=> DH-DT-DT-DH
please add a dummy parameter of multiplicity 3
for the pert types to your parameter set.
  -e.g. DH-DT-DT-DH 1 0.0 0.3.
(This is because multiple torsional potentials may apply to a
 single torsion, and each is perturbed individually in gibbs.)

Who could tell me how to solve it. Thank you very much for your help.

　　

Jiang
　　　　　　　　　　　　　　yjjiang_at_mail.shcnc.ac.cn
　　　　　　　　　　　　　　　　　2002-04-21