[gmx-users] choosing appropriate force field

[Justin Lemkul]

On 1/1/15 5:13 AM, elham tazikeh wrote:
> Dear Justin
> thanks for your help
>
> i used of *ATB server* for making *.itp* file for SAL (salicylic acid), as
> below:
>
> [ moleculetype ]
> ; Name   nrexcl
> _N4Y     3
> [ atoms ]
> ;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
>      1    OA    1    _N4Y    O10    1   -0.546  15.9994
>      2     H    1    _N4Y    H16    1    0.469   1.0080
>      3     C    1    _N4Y     C8    1    0.643  12.0110
>      4     O    1    _N4Y     O9    1   -0.566  15.9994      ;  0.000
>      5     C    1    _N4Y     C3    2   -0.221  12.0110
>      6     C    1    _N4Y     C2    2    0.388  12.0110
>      7    OA    1    _N4Y     O7    2   -0.604  15.9994
>      8     H    1    _N4Y    H15    2    0.437   1.0080      ;  0.000
>      9     C    1    _N4Y     C1    3   -0.266  12.0110
>     10    HC    1    _N4Y    H11    3    0.175   1.0080
>     11     C    1    _N4Y     C6    3   -0.049  12.0110
>     12    HC    1    _N4Y    H14    3    0.140   1.0080      ;  0.000
>     13     C    1    _N4Y     C5    4   -0.201  12.0110
>     14    HC    1    _N4Y    H13    4    0.141   1.0080
>     15     C    1    _N4Y     C4    4   -0.073  12.0110
>     16    HC    1    _N4Y    H12    4    0.133   1.0080      ;  0.000
> ; total charge of the molecule:   0.000
>

Note that ATB has chosen to protonate the carboxylic acid; this may not be 
correct.  The charges around the ring are all clearly inconsistent and will have 
to be corrected, but this framework of a topology is better than that of PRODRG 
since at least the aromatic ring is represented correctly.

>
> here, i have a question:
> in ATB server , there are 2 force field as default:* gromos 54A7 , gromos
> 53A6*
> i did not see other force field,right?

No idea.  Whatever they show is whatever is available.

> for my simulation, can i choose *gromos43a1* or i have to choosing the same
> force field (as ATB), i mean i must choose gromos 54A7?
>

You need to use the same force field.  If you want to use 43A1, the differences 
between the two are minimal and require only slight modifications to the 
charges.  Compare equivalent functional groups and you will see.

> on theother hand, Formats in ATB,were:
> Gromacs
> Gromos 11
> Gromos 96
>
> for my study, i choosed *Gromacs* as format in ATB , is it correct?
>

Well, if you're using Gromacs...

> finally, for SAL molecule ; there is SAL in ATB as default, and i used of
> it without loading of anywhere (same PRODRG)
> is this correct?
>

If they have a pre-calculated topology, it's probably judged as being reliable, 
so sure.  It's still up to you to evaluate whether or not it makes sense, by 
consulting any literature that has used it and by testing it yourself.

>
> at the end, shoul i  change *pdb* format (produced by ATB) to *gro* with
> *editconf* tool in gromacs and then *copy* et the end of my  protein
> coordinate file?
> or
> change my *complex.pdb* (get from RCSB) format to *coordinate.gro?*
>

Neither .pdb nor .gro is explicitly required, you can use whatever you like.

-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

==================================================