[gmx-users] unable to generate gro file -(only c alpha atoms -named as CB)

[mohan maruthi sena]

Hi all,
           My pdb file contains only c-alpha atoms , i have named alternate
CA atoms(res) as CB(1res CA,2res CB,3res CA...) , I have given my residue
name as ALB, accordingly i have changed .rtp ,atomtype
files,residuetype.dat. i want to use force field(charmm27.ff) present in
current directory using -ff option. These are the following errors that i
am getting while trying to generate .gro ,.top files using pdb2gmx

1)using the following command i got ,
     pdb2gmx -f 1ypi_ca_cb.pdb -o 1ypi.gro -p 1ypi.top -ff charmm27.ff
error: Could not find force field 'charmm27.ff' in current directory,
install tree or GMXDATA path.

2) when i used option export GMXLIB=/home/maruthi/1ypi to current directory

error:  atom N not found in buiding block 1ALB while combining tdb and rtp
 where as there are no N atom in my pdb file

3) when i used -ter option, and selected n-terminal none and c terminal
none , i got the following error,
           WARNING: atom CB is missing in residue ALB 240 in the pdb file


WARNING: atom CA is missing in residue ALB 241 in the pdb file


WARNING: atom CB is missing in residue ALB 242 in the pdb file


WARNING: atom CA is missing in residue ALB 243 in the pdb file


WARNING: atom CB is missing in residue ALB 244 in the pdb file


WARNING: atom CA is missing in residue ALB 245 in the pdb file


WARNING: atom CB is missing in residue ALB 246 in the pdb file


WARNING: atom CA is missing in residue ALB 247 in the pdb file


WARNING: atom CB is missing in residue ALB 248 in the pdb file

Fatal error:
There were 247 missing atoms in molecule Protein_chain_A, if you want to
use this incomplete topology anyhow, use the option -missing
For more information and tips for troubleshooting, please check the GROMACS

I do not understand what went wrong , i hope the options i have used are
correct. Please kindly suggest me a way to solve this.


Thank you in advance,

Regards,
Mohan
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