[gmx-users] OPLS-AA forcefield parameters
Jacob Harvey
j.harv8 at gmail.com
Sat Apr 4 21:09:10 CEST 2009
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:
"Fatal error:
Residue 'H' not found in residue topology database"
When I dont put anything in that column I get the error:
"Fatal error:
Residue '' not found in residue topology database"
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"
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> 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>
>>
>>
>> ------------------------------------------------------------------------
>>
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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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--
--
Jacob Harvey
Graduate Student
University of Massachusetts Amherst
j.harv8 at gmail.com
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