AMBER Archive (2005)

Subject: AMBER: average struct without solvent

From: C Balasubramanian (cbala_at_igib.res.in)
Date: Mon Nov 21 2005 - 07:51:26 CST

Dear users,

I hve run a 1.5ns simulation on a 12 mer DNA in explicit solvent with PBC. i wanted to calculate the average structure without (excluding) solvent and ions. the following is the input i gave to ptraj. I am getting the structure but it is highly scattered and not a proper one. Someone please help me on this.

trajin mde.mdcrd
trajin mdp1.mdcrd
trajin mdp2.mdcrd
average avgst.pdb pdb nowrap
center :1-24
image familiar
strip :WAT
strip :Na+

thanks,
Bala

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