Re: [gmx-users] pdb2gmx doesn´t generate H

2010-07-25 Thread Justin A. Lemkul
Oliver Grant wrote: Hi, This seems to be a problem with amber ports in gromacs. I believe it is because the residue attached to an N terminal residue. Try manually adding the hydrogen to the backbone nitrogen in the SER2 in the pdb. This solved the problem for me although there were repor

Re: [gmx-users] pdb2gmx doesn´t generate H

2010-07-24 Thread Oliver Grant
Hi, This seems to be a problem with amber ports in gromacs. I believe it is because the residue attached to an N terminal residue. Try manually adding the hydrogen to the backbone nitrogen in the SER2 in the pdb. This solved the problem for me although there were reports from other people of the

[gmx-users] pdb2gmx doesn´t generate H

2010-07-23 Thread Pascal Baumann
Hi I´m using GROMACS 4.0.7 with the Amber99sb forcefield. I keep getting an error when I´m typing this command: pdb2gmx -f t.pdb -o t2.pdb -ff amber99sb -water tip3p I get this message: WARNING: atom H is missing in residue SER 2 in the pdb file You might need to add atom H to the hydr