Ragnarok sdf wrote:
Hello. Ie been trying to run a DNA simulation with gromacs using amber99
force field. I've started with my DNA sequence complexed with the
protein, but then decided to separate them to know exactly what the
problem was. Now I am not even using the DNA sequence from my pdb file.
I`ve used the NAB server to create a DNA sequence which is exactly the
same as the one I had. I decided to do this in order to minimize the
problems with the amber forcefield. Well, that didn't work either.
I keep getting the "Error - No default Bond types.....no default angle
types....etc "
On a previous email I asked the same question, and the answer was. Take
a look at the lines where the error appears. Just to be more specific on
my problem.....ERROR 0 [file "1vkxdna_C.itp", line 71]:
No default Bond types
ERROR 0 [file "1vkxdna_C.itp", line 196]:
No default Angle types
Ok. I've taken the last advice and went ther to line 196. Except that on
line 196 there are 4 columns
"16 18 19 1" with values that I cannot spot the problem. I
went to the manual to see what each line means but came out without
knowing exactly what to do with them.
The listing there are the three atoms in the angle (ai, aj, ak) and the function
type. Descriptions of these are in Chapter 5 of the manual. Details are a bit
sparse regarding angles, but the text regarding other parameters and topology
format are more detailed, and generally applicable.
Other lines within the [ angles ] section should have angle parameter
information following the fourth column, but that line will not. Determine if
there should be, or if something else has gone wrong (see below).
Another problem I've spotted is that the charge (no matter what i try)
always comes out as a non integral value. I've renamed all atoms exactly
like they should be...one by one....really...one by one.
I would like some advice on the problem if possible.
Then something probably went wrong with topology creation, but that's very hard
to diagnose. Each residue (nucleotide) in the .top should end with an integer
charge (;qtot in the .top). See if this is breaking down, and if so, post one
of the nucleotides on the list if you can't find out what's wrong with it.
Also, please post your pdb2gmx command line from when you created the .top.
-Justin
Ps: The amber Dickerson test works out just fine.
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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