[gmx-users] gramicidin A
pragyachohan at hotmail.com
Sat Nov 3 08:33:58 CET 2007
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:
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
Just define the connectivity in the residue. Names prepended with a dash
("-") refer to atoms in the next residue, if present.
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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