[gmx-users] editbox removes dummy atoms

Hi everybody, I have an protein structure with many dummy atoms around it simulating the membrane around the protein. Those dummy atoms are signed in the file as an ATOM. When I want to put this protein with the membrane in a box with the command editconf -f 3m71.gro -o 3m71_box.gro -bt

Re: [gmx-users] editbox removes dummy atoms

On 6/28/12 10:11 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I have an protein structure with many dummy atoms around it simulating the membrane around the protein. Those dummy atoms are signed in the file as an ATOM. When I want to put this protein with the membrane

Re: [gmx-users] editbox removes dummy atoms

I have found out that there was always the same residue number for all the dummy atoms. Perhaps that was the failure. Now I changed it so that they have all different residue numbers. But now I get the error: Atom N is used in an interaction of type improper in the topology database, but an atom

Re: [gmx-users] editbox removes dummy atoms

On 6/28/12 10:40 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: I have found out that there was always the same residue number for all the dummy atoms. Perhaps that was the failure. Now I changed it so that they have all different residue numbers. But now I get the error: Atom N is