AMBER Archive (2008)

Subject: AMBER: How to build a dimer using amber

From: Reena ..... (ren.saini_at_gmail.com)
Date: Tue Jan 15 2008 - 01:19:45 CST

Hello amber users,

I am trying to build a dimer using monomers of polyglycine, but am somehow
unable to satisfy myself with the upcoming structure.
I have tried placing the "ter" card and the combine command in xleap. The
dimer no doubt is formed but I feel it will result in biased
result......coz the monomers in the structure thus formed will minimise/
stablise in each others vicinity. Also the monomers are always n the
parallel geometry whereas they can adopt a number of ways to form
dimer...say tail tail; head tail; head head geometry etc......I want to see
how the the two monomers will interact when put in a system say, solvent box
(water). And the same I want to study for highermers.....
I have also used Hex, wherein the resulting file had two monomers in
antiparallel geometry as the most stable structure. This file was used as
input structure for the minimisation n dynamics run in Amber.
I am new to the software....Please help!!!!!!!!!!!

thankyou

regards
Reena

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