[gmx-users] charge distriburion

[elham tazikeh]

Dear Justin
thanks for your replys

one of my most important problem is choosing correct pdb
in RCSB , there is not any pdb that consist of *Aspirin *+ HSA...and in
literature, using of *2i30* as pdb
my question is; should we use *docking software* for adding real Aspirin on
HSA or we can adding *ACE group to pdb file  (by hand*) or none of them?



finally, for pdb=2i30 , Atom section in my .itp file (produce by PRODRG0
was;

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1        OM     1  SAL     O1'     1   -0.765  15.9994 ;'
     2         C     1  SAL     C1'     1    0.354  12.0110 ;'
     3        OM     1  SAL     O2'     1   -0.765  15.9994 ;'
     4         C     1  SAL      C1     1   -0.027  12.0110
     5       CH2     1  SAL      C6     1    0.102  14.0270
     6       CH2     1  SAL      C5     1    0.101  14.0270
     7       CR1     1  SAL      C4     2    0.010  13.0190
     8       CR1     1  SAL      C3     2    0.010  13.0190
     9         C     1  SAL      C2     2    0.130  12.0110
    10        OA     1  SAL      O2     2   -0.191  15.9994
    11         H     1  SAL      H2     2    0.041   1.0080

by advising your good  ideas, i saw in aminoacids.rtp for charge(s) and i
reached to below cherges:

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1        OM     1  SAL     O1'     1   *-0.635*  15.9994 ;'
     2         C     1  SAL     C1'     1    *0.38*  12.0110 ;'
     3        OM     1  SAL     O2'     1  * -0.635*  15.9994 ;'
     4         C     1  SAL      C1     1    *0*  12.0110
     5       CH2     1  SAL      C6     1    *-0.1*  14.0270
     6       CH2     1  SAL      C5     1    *-0.1*  14.0270
     7       CR1     1  SAL      C4     2    *-0.1*  13.0190
     8       CR1     1  SAL      C3     2    *-0.1*  13.0190
     9         C     1  SAL      C2     2   * 0.15*  12.0110
    10        OA     1  SAL      O2     2   *-0.548*  15.9994
    11         H     1  SAL      H2     2   * 0.398*   1.0080


As showed in above table, the sum of chares are not still  Zero (even with
assuming H s ring)
please watch to them and give me help...

on the other hand, there are 2 molecules of SAL in pdb file that which one
have 10 atoms and in .itp file i achieved 11 atoms.is this correct?

Regards