Re: [gmx-users] question about pdb2gmx

On 7/19/12 6:28 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: There is only one Cystein: ATOM 1797 N CYS A 211 10.568 1.888 4.891 1.00 1.00 ATOM 1798 CA CYS A 211 11.782 1.312 5.391 1.00 1.00 ATOM 1799 CB CYS A 211 12.968 1.606 4.452 1.00

Re: [gmx-users] question about pdb2gmx

There is only one Cystein: ATOM 1797 N CYS A 211 10.568 1.888 4.891 1.00 1.00 ATOM 1798 CA CYS A 211 11.782 1.312 5.391 1.00 1.00 ATOM 1799 CB CYS A 211 12.968 1.606 4.452 1.00 1.00 ATOM 1800 SG CYS A 211 14.599 1.282 5.172 1.00 1.00 AT

Re: [gmx-users] question about pdb2gmx

On 7/19/12 6:17 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, thank you for your answer. I already tried the -ss command but nothing happens. The program just writes the topology file but it does not ask me anything. My command was: pdb2gmx -f protOnly.pdb -o 3m71.gro -p 3

Re: [gmx-users] question about pdb2gmx

Hi Justin, thank you for your answer. I already tried the -ss command but nothing happens. The program just writes the topology file but it does not ask me anything. My command was: pdb2gmx -f protOnly.pdb -o 3m71.gro -p 3m71.top -ss -water tip3p -ff amber03 is there something wrong with this com

Re: [gmx-users] question about pdb2gmx

On 7/19/12 5:00 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to add protonation states to my protein with pdb2gmx. I now that there are the options: -lys -arg -asp -glu -his to do this. But was is about the cystein. How can I protonate this one? Is there also

[gmx-users] question about pdb2gmx

Hi everybody, I want to add protonation states to my protein with pdb2gmx. I now that there are the options: -lys -arg -asp -glu -his to do this. But was is about the cystein. How can I protonate this one? Is there also an option for it which I haven't seen? Thank you , Eva -- gmx-users mail