[gmx-users] OPLS-AA forcefield parameters
Justin A. Lemkul
jalemkul at vt.edu
Sat Apr 4 22:22:32 CEST 2009
Jacob Harvey wrote:
> Justin,
>
> How do I go about running topolgen on a linux system? There doesn't seem
> to be instructions for use, but I'm not familiar with perl scripts. Also
> I'd just like to say thank you for all your help. You've been really
> good with responding to my e-mail. I know that you have referenced
> chapter 5 in the manual multiple times, and I can assure you that I have
> read that chapter several times. I am a first year graduate student who
> is very new to molecular dynamics so some of the material is not trivial
> to me. Thank you again!
>
To execute:
perl topolgen.pl input.pdb
Guess I forgot to include that in the README; my mistake. I'm working on making
the script better, so I'll update that for a future release. Also be warned
that I have not extensively tested the script beyond some basic small molecules.
Please run some test simulations before collecting any real data.
There are also a number of tutorials on the Gromacs wiki. The one written by
Tsjerk is especially good at diagramming the flow of the programs, input/output,
and how everything is put together. If you are unfamiliar with Gromacs, try out
some tried-and-true methodology on known systems before simulating some bizarre
system. It will save you a lot of headaches.
-Justin
> Jacob Harvey
>
> On Sat, Apr 4, 2009 at 3:17 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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>>
> <mailto: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> <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>
> <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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the www
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> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> --
> --
> Jacob Harvey
>
> Graduate Student
>
> University of Massachusetts Amherst
>
> j.harv8 at gmail.com <mailto:j.harv8 at gmail.com>
--
========================================
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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