Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

Dear Justin, The command line that got fatal error is: gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh -merge interactive The command line that works fine is: gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water spce -inter -ignh -merge interactive (just

Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

On 5/19/17 6:31 PM, ZHANG Cheng wrote: Dear Justin, I replied the thread already, but it is waiting for approval due to large email content. Could you please approve it? I have no control over that. If it's too much for an email (normally pdb2gmx output is fine) then upload to e.g.

Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

Dear Justin, I replied the thread already, but it is waiting for approval due to large email content. Could you please approve it? Cheng ---Original--- From: "ZHANG Cheng"<272699...@qq.com> Date: 2017/5/19 22:37:52 To: "gromacs.org_gmx-users"; Cc:

Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

On 5/19/17 5:37 PM, ZHANG Cheng wrote: Dear Gromacs, I got this fatal error after running "pdb2gmx": Please provide your exact command and full screen output. There's a lot of relevant information there, because pdb2gmx is doing a lot of complex things. -Justin Fatal error: Residue 1

[gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

Dear Gromacs, I got this fatal error after running "pdb2gmx": Fatal error: Residue 1 named ASP of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be