[gmx-users] No default U-B types in CHARMM36 FF

[Albert]

IC.

I run it again, and select all the options as none. However, it claimed 
that hydrogens in NMA is missing. shouldn't pdb2gmx add hydrogens to 
residues automatically?

End terminus NMA-339: None
Opening force field file 
/soft/gromacs-4.6.5/share/gromacs/top/charmm36-mar2014.ff/merged.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 305 residues with 4847 atoms
Making bonds...

WARNING: atom H is missing in residue NMA 339 in the pdb file
          You might need to add atom H to the hydrogen database of 
building block NMA
          in the file merged.hdb (see the manual)


WARNING: atom HH31 is missing in residue NMA 339 in the pdb file
          You might need to add atom HH31 to the hydrogen database of 
building block NMA
          in the file merged.hdb (see the manual)


WARNING: atom HH32 is missing in residue NMA 339 in the pdb file
          You might need to add atom HH32 to the hydrogen database of 
building block NMA
          in the file merged.hdb (see the manual)


WARNING: atom HH33 is missing in residue NMA 339 in the pdb file
          You might need to add atom HH33 to the hydrogen database of 
building block NMA
          in the file merged.hdb (see the manual)


-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.5
Source code file: /home/albert/gromacs-4.6.5/src/kernel/pdb2top.c, line: 
1588

Fatal error:
There were 4 missing atoms in molecule Protein_chain_X, if you want to 
use this incomplete topology anyhow, use the option -missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"One Cross Each" (Monty Python)



On 04/13/2014 07:17 PM, Justin Lemkul wrote:
> Your ending terminus should be None, not 3TER.  3TER is for nucleic 
> acids.