Re: [gmx-users] adding hydrogens to protein with pdb2gmx

2012-09-05 Thread reisingere
Hi Marcelo, thanks a lot for your help!! > After doing the 'pdb2gmx', created the cell e filled with solvent, use the > "make_ndx" to create an index of your system. One of the groups should be > your residues that you want to freeze. Then, in your .mdp file, use > 'freezegrps' and 'freezedim' in

Re: [gmx-users] adding hydrogens to protein with pdb2gmx

2012-09-04 Thread Marcelo Depolo
After doing the 'pdb2gmx', created the cell e filled with solvent, use the "make_ndx" to create an index of your system. One of the groups should be your residues that you want to freeze. Then, in your .mdp file, use 'freezegrps' and 'freezedim' in your recently created group. Don't forget the -n

Re: [gmx-users] adding hydrogens to protein with pdb2gmx

2012-09-04 Thread Justin Lemkul
On 9/4/12 11:59 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Yes okey. I understood. But I have another question: Since I only want to minimize the phosphates which I added to the protein I want to use the freeze option to make sure that the other residues will not change. But how

Re: [gmx-users] adding hydrogens to protein with pdb2gmx

2012-09-04 Thread reisingere
Yes okey. I understood. But I have another question: Since I only want to minimize the phosphates which I added to the protein I want to use the freeze option to make sure that the other residues will not change. But how can I say gromacs that it shell make an exception and do not freeze the phos

Re: [gmx-users] adding hydrogens to protein with pdb2gmx

2012-09-04 Thread reisingere
Okey, Thank you!! > Only the -ignh flag is wrong, as Justin said. > > Keep the rest of the command line. > -- > Marcelo Depólo > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Su

Re: [gmx-users] adding hydrogens to protein with pdb2gmx

2012-09-04 Thread reisingere
But the rest of the command was correct? Since I only want to minimize the phosphates which I added to the protein I want to use the freeze option to make sure that the other residues will not change. But how can I say gromacs that it shell make an exception and do not freeze the phosphate of the

Re: [gmx-users] adding hydrogens to protein with pdb2gmx

2012-09-04 Thread Marcelo Depolo
Only the -ignh flag is wrong, as Justin said. Keep the rest of the command line. -- Marcelo Depólo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before post

Re: [gmx-users] adding hydrogens to protein with pdb2gmx

2012-09-04 Thread Justin Lemkul
On 9/4/12 11:21 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, when I want the program "pdb2gmx" only to create a topology file but not to change anything at the protein. Not even adding hydrogen atoms to the protein. Because my protein already has hydrogen atoms. I only

[gmx-users] adding hydrogens to protein with pdb2gmx

2012-09-04 Thread reisingere
Hi everybody, when I want the program "pdb2gmx" only to create a topology file but not to change anything at the protein. Not even adding hydrogen atoms to the protein. Because my protein already has hydrogen atoms. I only added one residue and I want to minimize this residue now. Do I have to ca