[gmx-users] Pdb2gmx with Amber99SB-ILDN

[Justin A. Lemkul]

Alberto Arrigoni wrote:
> Dear gmx-users,
> I encountered a problem using pdb2gmx with Amber99SB-ILDN when I tried 
> to use the -ter flag in order to select "none" as termini state.
> Pdb2gmx simply ignores -ter, and doesn't prompt the list of entries for 
> termini selection.
> 
> Has anyone else had this kind of problem?
>         

This is the way the AMBER force fields work; they are different from all the 
others.  All potential terminal residues and caps are listed in the 
aminoacids.rtp file.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================