[gmx-users] choosing appropriate force field
jalemkul at vt.edu
Thu Jan 1 16:41:43 CET 2015
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
> [ 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
> 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:
> 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?
> 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 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
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