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 <[email protected]
<mailto:[email protected]>> 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
[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
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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
[email protected] <mailto:[email protected]>
--
========================================
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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