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 fix
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
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: "QQ"<272699...@qq.com>;
Subject: pdb2gmx: At
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. pasteb
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 change