Re: [gmx-users] interchain bond

2008-01-16 Thread Jochen Hub
Xavier Periole wrote: On Tue, 15 Jan 2008 16:32:54 +0100 Velia Minicozzi [EMAIL PROTECTED] wrote: Dear gromacs users, I have two identical peptides which should bind one metal ion. I guess I have not understood how I can make this bond. I labeled the two peptides with different chain

Re: [gmx-users] interchain bond

2008-01-16 Thread Velia Minicozzi
Thank you Xavier, but I still have problems because when I use merge, pdb2gmx doesn't want that the second peptide has NH3+ and COO- as terminals and doesn't understand if I use -ter when I am using -merge, so doesn't create the top file. What do you exactly mean for the numbering of atoms

Re: [gmx-users] interchain bond

2008-01-16 Thread Xavier Periole
On Wed, 16 Jan 2008 22:29:31 +0100 (CET) Velia Minicozzi [EMAIL PROTECTED] wrote: Hi Xavier, I think it works I just deleted the 3 H at the N-terminus of the second chain and when I used merge in pdb2gmx it worked! Thanks a lot! Cool. What I meant with the atom numbers is that now you can

[gmx-users] interchain bond

2008-01-15 Thread Velia Minicozzi
Dear gromacs users, I have two identical peptides which should bind one metal ion. I guess I have not understood how I can make this bond. I labeled the two peptides with different chain identifier otherwise pdb2gmx does not understand that they are two peptides and not one protein. The metal

Re: [gmx-users] interchain bond

2008-01-15 Thread Xavier Periole
On Tue, 15 Jan 2008 16:32:54 +0100 Velia Minicozzi [EMAIL PROTECTED] wrote: Dear gromacs users, I have two identical peptides which should bind one metal ion. I guess I have not understood how I can make this bond. I labeled the two peptides with different chain identifier otherwise pdb2gmx