PDB format has fixed column widths. You cannot edit it correctly unless you
preserve the layout - e.g. replace deleted characters with spaces.
Mark
On Nov 28, 2013 4:26 AM, "kolnkempff" wrote:
> /I am trying to use pdb2gmx to get a topology for a very simple peptide
> that
> has just three compo
/I am trying to use pdb2gmx to get a topology for a very simple peptide that
has just three components: an ACE residue followed by phenylananine
followed by NME
I've read through the Duan article and it seems that amber03 should be ideal
for this. The pdb file I'm using came from a quantum simula