[AMBER] constant pH simulation (protonation state specification)

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Sun, 13 Jun 2010 21:46:34 +0530 (IST)

Hello all

I am doing constant pH simulation at pH 4 .Should I specify the -states flag for
generation of cpin file?

In manual by default protonation state is 0: which specify
deprotonated for ASP and GLU, protonated for LYS and TYR, doubly protonated for
HIS (i.e. HIP).

In example there is other protonation state 1, 3:

ambpdb -p prmtop < prmcrd | cpinutil.pl -states 1,3,0,0,0,1 > cpin

So what is mean by protonation state 1, 3

Can I specify both -state & -system flag during generation of cpin file?

Seeking for suggestion.

With regard
Sangita Kachhap

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Received on Sun Jun 13 2010 - 09:30:06 PDT
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