AMBER Archive (2003)

Subject: AMBER: about some of the cards in Sander 7

From: Pingna Xu (px208_at_nyu.edu)
Date: Wed Nov 12 2003 - 14:09:12 CST

Hi,

I want to run molecular dynamics for protein-DNA system using Sander in Amber7.I have noticed that in Sander7,there are only options 1-6 for the card "NTX".But I want to set NTX=7 for the MD.Is that OK?
And I also found that in Sander7,there is no "npscal" or "ndfmin" anymore.But the guys in our lab always set ndfmin=6 and npscal=1 for the MD since they use earlier versions of Amber.What should I do with these two cards since I am using Amber7?Thanks!

Pingna

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