Monday, April 20, 2009

step closer to GROMACS and Carbon nanotubes, or some ramblings

Okay I figured out why I was getting all the short bond errors when I ran pdb2gmx (see previous post). I came across this paragraph in the gmx wiki:

"One point that is not made clearly in the manual is how to specify the connectivity between residues. This mechanism is protein-specific, and relies on the existence in each residue of atoms with the same names, i.e. the protein backbone atoms. The [ bonds ] section in the example in section 5.6.1 of the manual defines a bond between -C and N. This refers to the C atom in the previous residue. Similarly, one might use a +N prefix to refer to the N atom in the following residue."

This meant I never defined how the residues were connected together in my .rtp file. This explains why I got a bunch of short bond warnings and my topology file never had pairs, angles or dihedrals.

I've changed the [bonds] section of the .rtp from the cnt carbons to:

NT1 ]
C C 0 0

C C 0 0

[ bonds ]
C +C 0.14210 478900

However I can't be certain that adding a +C to the second C in all the bonds makes sense for all of them. I guess I need to know how you put together a large protein and then figure out how you assemble a carbon nanotube using the same basic steps...

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