DNA-linker atom not recognized

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1

GROMACS version:
GROMACS modification: Yes/No
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Hi,
I’m stuck at a really stupid problem.
When I’m trying to execute pdb2gmx with a DNA (using amber99sb-ildn forcefield) I’m getting an error as :

Fatal error:
Atom C01 in residue DG 3 was not found in rtp entry DG with 33 atoms
while sorting atoms.

I understand that atom description does not match the forcefield description.
I have manually added 4 carbon, 3 oxygen and 1 phosphate atoms (using pymol Builder) to the DNA’s Guanosine (as a part of my linker experiment).
Is there any way I can make the forcefield to treat them as simple carbon, oxygen and phosphate atoms to continue with the simulation procedure?

Please suggest.

2

Atom names have to match what is expected in the .rtp entry corresponding to that residue. There is no way to force pdb2gmx to accept “generic” atoms because they have to be mapped to known atom names to generate the bonded structure.

3

Can you please suggest a way to deal with covalently linked linkers in gromacs ?
The DNA’s G base is covalently linked with C4O2P linker.
If I need to use it for simulation, should I name it as a different residue (so that .rtp does not find a conflict with Guanosine parameters)?

Please advise.
Thank you.

4

Such a species will not be present in the force field so you will have to parametrize the residue and add it to the force field.

http://manual.gromacs.org/current/how-to/topology.html#adding-a-new-residue