[gmx-users] Issues with my PDB file
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 2 22:59:55 CEST 2009
Jacob Harvey wrote:
> Justin,
>
> Thank you for your response. I figured this was the problem actually and
> tried renaming things a little bit but I got confused and my file still
> didn't work. I'll try and dig that file up to show you, but what exactly
> do I need to rename and if I want to use the OPLS-AA force field what do
> I need to rename things to. Is it the opls_XXX atoms in the .atp file?
> Where is it getting "residue 2" from? Is that from the atom number 2 or
> the two columns of 2's next to the atom name (ie. C,N,H)? I'm not sure I
> understand the structure of a pdb file. Thank you very much for your
> response.
>
I would suggest some tutorial material on a well-defined protein or some other
simple system. See the wiki for some examples about how to start without diving
head-first into a bizarre example that may not work.
Wiki: http://wiki.gromacs.org/index.php/Main_Page
PDB file format: http://www.wwpdb.org/documentation/format32/sect9.html
Note as well that pdb2gmx will only work on building block compounds (proteins,
nucleic acids, and a limited set of cofactors, generally - this depends on the
force field). So if you expect pdb2gmx to be magic, expect to be disappointed.
-Justin
> Jacob
>
> On Thu, Apr 2, 2009 at 3:13 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Jacob Harvey wrote:
>
> Dear all,
>
> I appear to be having problems with my pdb file for gromacs. If
> someone could help me out that would be awesome. I enter the
> following code to run pdb2gmx:
>
> pdb2gmx -f test.pdb
>
> and then I select a force field. I have selected OPLS-AA/L
> all-atom force field (2001 aminoacid dihedrals). Once I select
> the force field I get the error
>
> "Fatal error:
> Residue '2' not found in residue topology database"
>
>
> That one's pretty self-explanatory. You can't expect pdb2gmx to be
> magic. Parameters have to exist in the force field .rtp file for
> each building block you want to use. A residue named "2" is
> meaningless to pdb2gmx.
>
> -Justin
>
> This is what my pdb file looks like (I've just posted the first
> 10-15 lines or so). Does anyone see where I am going wrong?
> Thank you very much in advance.
>
> HETATM 1 C 2 2 -4.438 3.334 2.988
> HETATM 2 C 2 2 0.588 3.313 0.517
> HETATM 3 C 2 2 5.476 3.310 -2.216
> HETATM 4 H 2 2 -4.134 2.590 3.731
> HETATM 5 H 2 2 -5.525 3.438 3.047
> HETATM 6 H 2 2 -3.996 4.291 3.276
> HETATM 7 H 2 2 1.480 3.111 1.117
> HETATM 8 H 2 2 -0.266 3.349 1.200
> HETATM 9 H 2 2 0.702 4.307 0.076
> HETATM 10 H 2 2 6.375 3.525 -1.633
> HETATM 11 H 2 2 4.648 3.862 -1.761
> HETATM 12 H 2 2 5.628 3.709 -3.223
> HETATM 13 C 2 2 -3.996 2.922 1.581
> HETATM 14 H 2 2 -2.902 2.862 1.545
> HETATM 15 H 2 2 -4.281 3.703 0.865
> HETATM 16 C 2 2 0.394 2.242 -0.557
> HETATM 17 H 2 2 -0.485 2.486 -1.167
> .
> .
> .
> .
> .
>
> 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>
--
========================================
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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