[gmx-users] charge distriburion

[Justin Lemkul]

On 12/31/14 2:35 AM, elham tazikeh wrote:
> 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?
>

Either approach should work.  Docking would probably be more conventional.

>
>
> 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...
>

You're assigning C charges as if the H were there; aromatic H have +0.1e to 
balance the charge on the C atom.  As I said before, CH2 is flat-out wrong for 
this structure - PRODRG has given you a totally incorrect topology.  No amount 
of hacking the charges will correct this error.  It is an aromatic ring; there 
are no CH2.  Try generating something more sensible with ATB.

> 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?
>

Consider which elements are usually missing in crystal structures.  The 
difference here should be obvious upon inspection of the contents of the .pdb file.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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