AMBER Archive (2001)

Subject: charge on protein

From: Giulio Rastelli (giulio_at_caesar.unimo.it)
Date: Wed Aug 15 2001 - 12:08:43 CDT

Dear all,

-I am running a MD simulation of a protein in a periodic box of water
using PME. The protein has a net charge of -11. Should I neutralize
the protein with counterions (using leap?) before running PME MD?
Is this correct? I saw that PME forces neutrality by itself...

-Is a box 9Angstrom away from every atom of the protein enough for
properly account solvation?

-Since PME calculations on my protein (230AA + 9600WAT) are very
slow on a IBM-SP3 (4procs used), I would like to hear somebodyelse
experience using PME, PBC on proteins...

Thanks in advance,

Giulio

Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Universita di Modena e Reggio Emilia
Via Campi 183
41100 Modena - ITALY
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tel 0039-059-2055145
fax 0039-059-2055131
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