hi
I was trying to run pdb2gmx command for gramicidin and noticed it has some
D-amino acids. Reading the earlier mail wjich states that:
It's not too difficult to add a new residue to the topology database.
Have a look in the file ff.rtp, where is the force field
you are using.
You can probably copy most parts from a standard amino acid that is
similar to your new one. There are three parts for each residue:
[atoms]
This section maps names found in the pdb file (col 1) to atom types (col
2), charge (col 3) and charge groups (col 4). Try to have neutral charge
groups.
[bonds]
Just define the connectivity in the residue. Names prepended with a dash
("-") refer to atoms in the next residue, if present.
[impropers]
Define the improper dihedrals needed to maintain chirality of the molecule.
That's it - everything else like angles, normal dihedrals, and the
actual parameters will be generated by pdb2gmx.
I generated .itp from prodrg server and included the above stated things in
.rtp file. But again when i ran pdb2gmx i got the same error..
Residue 'DLE' not found in residue topology database.
What should i do? if anyone has topology file for gramicidin please send me
Thanks in advance
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