Re: [gmx-users] Problem importing PDB to Gromacs

2013-05-12 Thread tarak karmakar
Remove all the hydrogens from the pdb file and then try to run pdb2gmx, I hope it'll do fine. Or you can also use -ignh option as suggested by Justin. Tarak On Fri, May 10, 2013 at 3:35 PM, Justin Lemkul wrote: > > > On 5/10/13 5:16 AM, Jernej Zidar wrote: > >> Hi, >>In CHARMM I generated

Re: [gmx-users] Problem importing PDB to Gromacs

2013-05-10 Thread Justin Lemkul
On 5/10/13 5:16 AM, Jernej Zidar wrote: Hi, In CHARMM I generated a short peptide. The N-terminal is a regular -NH2 (patch NNEU) while the C-terminal is amidated (patch CT2). I would like to import the PDB to GROMACS using pdb2gmx by using the CHARMM27 forcefield later. I issue the foll

[gmx-users] Problem importing PDB to Gromacs

2013-05-10 Thread Jernej Zidar
Hi, In CHARMM I generated a short peptide. The N-terminal is a regular -NH2 (patch NNEU) while the C-terminal is amidated (patch CT2). I would like to import the PDB to GROMACS using pdb2gmx by using the CHARMM27 forcefield later. I issue the following command: pdb2gmx -v -f irik-l.pdb -inte