[gmx-users] change atom type in ffbonded.itp

‪sky sky‬ ‪ sky8801 at yahoo.com
Sat Nov 5 15:35:42 CET 2016

Hi justin.
Excuse me ask you againI attached my residue topology file in this e-mail.I geting this information from cgenff server and include in the force field (charmm27).I have this error:
ERROR 1 [file ffbonded.itp, line 259]:  Not enough parameters
CGENFF does not geve me information related to ub0 and cub so, I changed ub0 and cub parts in ffbonded.itp.so no errors.ubo= 0.00cub= 0.00Now.I can change this infomations?If no,so how can i geting information related ubo and cub in ffbonde.itp?How to can generate this numbers?What is cth ,ub0 and cub ??
tanks a lot.
      From: Mostafa Khedrinia <mostafakhedrinia at gmail.com>
 To: gromacs.org_gmx-users at maillist.sys.kth.se 
 Sent: Tuesday, 1 November 2016, 15:10:32
 Subject: [gmx-users] change atom type in ffbonded.itp

I'm using Gromacs with
charm27.ff force-field.I adding a new residue (NAG) in force field

I have a problem with water molecules in my system: During
minimization, I have this message:

step X: Water molecule starting at atom XXX can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

My problem is related to protein structure.I changed angletypes part in
 ffbonded.itp .  so not errors.
my question:
This change how much is true?

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