[gmx-users] OPLS-AA forcefield parameters
Justin A. Lemkul
jalemkul at vt.edu
Sat Apr 4 21:17:02 CEST 2009
Jacob Harvey wrote:
> Thank you for your help Justin. I have corrected my naming problem in
> the pdb file. However, I am still getting errors. It does not seem to
> recognize the residues. BUT I dont actually have "residues" in my
> system, because I am not modeling a protein. So I am not sure what to
> put in the residue name column. Gromacs does work on molecules that are
> not proteins correct? My molecules are histidine like so I tried putting
> HIS as the residue name, but I got the error:
>
If you want to use pdb2gmx to automatically generate your topology, you have to
ensure that the appropriate .rtp entry is present within the desired force field
and has the same name as the building block you are trying to use (again, this
is spelled out in Chapter 5 of the manual). If you call your molecule "HIS,"
then pdb2gmx will not magically build a random molecule; it will try to build
histidine, based on the [ HIS ] entry in the .rtp file, so it will look for the
exact atomic entries for histidine, no more no less.
If you want a topology for an arbitrary molecule, you *can not* use pdb2gmx
(unless you build the .rtp entry yourself). You will have to build it by hand,
or use another program to build the .top file. I just uploaded a script I wrote
to build an OPLS-AA topology from a .pdb file to the Users Contributions section
on the website, but it does not assign atom types or charges (yet); it is up to
you to assign the parameters and verify them.
> "Fatal error:
> Residue 'H' not found in residue topology database"
>
Because it is not histidine.
> When I dont put anything in that column I get the error:
>
> "Fatal error:
> Residue '' not found in residue topology database"
>
Because of a formatting error (the fact that your residue is either blank, or
the number 2).
> And when I just generically call everything solvent and put SOL in that
> column I get:
>
> "Fatal error:
> Residue 'S' not found in residue topology database"
>
Probably another formatting issue. But none of the above actually solve your
problem, you're just trying to fool pdb2gmx into being magic, which it is not.
-Justin
> You get the picture here. Does anyone have any solutions to my residue
> naming problem? Thank you.
>
> here is my pdb file:
>
> HETATM 1 CT 2 -4.438 3.334 2.988
> HETATM 2 CT 2 0.588 3.313 0.517
> HETATM 3 CT 2 5.476 3.310 -2.216
> HETATM 4 HC 2 -4.134 2.590 3.731
> HETATM 5 HC 2 -5.525 3.438 3.047
> HETATM 6 HC 2 -3.996 4.291 3.276
> HETATM 7 HC 2 1.480 3.111 1.117
> HETATM 8 HC 2 -0.266 3.349 1.200
> HETATM 9 HC 2 0.702 4.307 0.076
> HETATM 10 HC 2 6.375 3.525 -1.633
> HETATM 11 HC 2 4.648 3.862 -1.761
> HETATM 12 HC 2 5.628 3.709 -3.223
> HETATM 13 CT 2 -3.996 2.922 1.581
> HETATM 14 HC 2 -2.902 2.862 1.545
> HETATM 15 HC 2 -4.281 3.703 0.865
> HETATM 16 CT 2 0.394 2.242 -0.557
> HETATM 17 HC 2 -0.485 2.486 -1.167
> HETATM 18 HC 2 1.250 2.252 -1.242
> HETATM 19 CT 2 5.188 1.805 -2.247
> HETATM 20 HC 2 6.018 1.286 -2.742
> HETATM 21 HC 2 4.300 1.615 -2.864
> HETATM 22 CT 2 -4.587 1.582 1.127
> HETATM 23 HC 2 -5.682 1.638 1.161
> HETATM 24 HC 2 -4.298 0.792 1.828
> HETATM 25 CT 2 0.235 0.836 0.028
> HETATM 26 HC 2 -0.616 0.818 0.720
> HETATM 27 HC 2 1.117 0.581 0.625
> HETATM 28 CT 2 4.981 1.206 -0.852
> HETATM 29 HC 2 4.152 1.720 -0.350
>
> Jacob Harvey
>
> On Sat, Apr 4, 2009 at 2:29 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Jacob Harvey wrote:
>
> Dear All,
>
> I am trying to use the OPLS-AA force field to model some
> imidazole containing compounds. I've noticed that imidazole
> units are referenced in the ffoplsaa.atp file as the following:
>
> opls_557 14.00670 ; N1 in imidazole
> opls_558 12.01100 ; C2 in imidazole
> opls_559 14.00670 ; N3 in imidazole
> opls_560 12.01100 ; C4 in imidazole
> opls_561 12.01100 ; C5 in imidazole
> opls_562 1.00800 ; H1 in imidazole
> opls_563 1.00800 ; H2 in imidazole
> opls_564 1.00800 ; H4 in imidazole
> opls_565 1.00800 ; H5 in imidazole
>
> But there are no parameters for these atoms in the ffoplsaa.rtp
> file. Does anyone know how I can go about naming these atoms in
> my pdb file? Thank you in advance.
>
>
> Not every compound is present in a .rtp file. Check out its
> contents and you'll see what it has - pretty much just amino acids.
> The charges on each atom are not specific to an atom type, they are
> specific to a chemical species for which the parameterization scheme
> has been conducted. Lennard-Jones parameters are specified in
> ffoplsaanb.itp.
>
> I suggest a thorough read of Chapter 5 of the manual to understand
> the contents of these database-type files, and how they are used in
> assembling a topology.
>
> -Justin
>
> Jacob Harvey
>
> --
> --
> Jacob Harvey
>
> Graduate Student
>
> University of Massachusetts Amherst
>
> j.harv8 at gmail.com <mailto:j.harv8 at gmail.com>
> <mailto:j.harv8 at gmail.com <mailto:j.harv8 at gmail.com>>
>
>
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> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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>
>
>
> --
> --
> Jacob Harvey
>
> Graduate Student
>
> University of Massachusetts Amherst
>
> j.harv8 at gmail.com <mailto:j.harv8 at gmail.com>
>
>
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>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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