Re: Θέμα: Re: Θέμα: Re: [gmx-users ] cyclic peptides

2006-08-19 Thread David van der Spoel
Efi Mantzourani wrote: Ok, tried the specbond. That doesn't work on its own. So I changed the forcefield N-terminus database (*.tdb) to give me an extra option for the terminus, [NH]. It seems to work fine, places the hydrogen in the peptide bond, but doesn't know anything about bond angles and

Θέμα: Re: Θέμα: Re: [gmx-users] cyclic peptides

2006-08-19 Thread Efi Mantzourani
Ok, tried the specbond. That doesn't work on its own. So I changed the forcefield N-terminus database (*.tdb) to give me an extra option for the terminus, [NH]. It seems to work fine, places the hydrogen in the peptide bond, but doesn't know anything about bond angles and dihedrals containing the n

RE: Θέμα: Re: [gmx-users] cyclic peptides

2006-08-17 Thread Mu Yuguang (Dr)
, August 17, 2006 10:51 PM To: Discussion list for GROMACS users Subject: Re: Θέμα: Re: [gmx-users] cyclic peptides Efi Mantzourani wrote: > Hi David, > > had a look for the specbond entry, but apparently it is for creating a > bond between ligand and receptor. I don't have th

Θέμα: Re: [gmx-users] cyclic peptides

2006-08-17 Thread Efi Mantzourani
Hi David,had a look for the specbond entry, but apparently it is for creating a bond between ligand and receptor. I don't have that. Mine is not a special bond. it is just that pdb2gmx tries to find a terminus for all the chains. David van der Spoel <[EMAIL PROTECTED]> έγραψε: Efi Mantzoura