[gmx-users] selection of start or end terminus

[Alexander Alexander]

Dear Gromacs user,

In the selection of start or end terminus type for peptide in OPLS_AA force
field, what is the diffeece between option 0 and 1 in below list? I am
interested in the Zwitterion form, but the option 0 is Zwitterion form if I
am not wrong!


Select start terminus type for ....
 0: NH3+
 1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
residue)
 2: NH2
 3: None

And why choosing 1 introduces a tiny amount of charge (0.010 e) in the
system and then the whole system in not neutral anymore but 0 is fine. It
is clear below the differences and origination of the extra charge in
\alpha-C, but how can I fix this if I want to choose 1? Can I simply edit
the topol file by replacing the opls_299 to opls_283 ... .?


Choosing 0.  :-)

; residue   1 LEU rtp LEU  q +1.0
  5  opls_293B      1    LEU     CA      1        0.25     12.011

 ;residue   7 GLU rtp GLU  q -2.0
 112   opls_283      7    GLU     CA     37       0.04     12.011


Choosing 1.   :-(

;residue   1 LEU rtp LEU  q +0.9
   5   opls_299      1    LEU     CA      1         0.15     12.011

;residue   7 GLU rtp GLU  q -1.9
112   opls_299      7    GLU     CA     37       0.15     12.011

Many thanks.
Regards,
Alex