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]>
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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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