Re: [gmx-users] topology for small peptide using amber03

2013-11-28 Thread Mark Abraham
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

[gmx-users] topology for small peptide using amber03

2013-11-27 Thread kolnkempff
/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