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
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