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

[Justin A. Lemkul]

On 5/22/12 9:24 PM, mohan maruthi sena wrote:
> 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.
>

If you want a CA-only model of a protein, you can't do it with CHARMM or any 
force field in Gromacs.  This force field (and all the others) are atomistic, 
and expect all the atoms to be present explicitly.  The error messages indicate 
as much.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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