[gmx-users] How to neutralize a protein

Jia-Lin Lo jllo at phy.ncu.edu.tw
Tue Jun 10 04:56:01 CEST 2003

Dear gmx_users;
    I have a pdb file with net charge +4. How would I neutralize it?
I have tried "protonate" this program. And I don't think it works if I use -ignh option in pdb2gmx command. 
    By thw way,I try to use PME method. Will it  
make big differences that the net charge isn't zero? 
     Thanks for helping me to solve these questions.

Jia-lin Lo
Dept. of Physics ,National Central University,
Chung Li , Taiwan,
e-mail : jllo at phy.ncu.edu.tw  Home page: http://pooh.phy.ncu.edu.tw/~jllo/
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