Hi all,<br> 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<br>
<br>1)using the following command i got ,<br> pdb2gmx -f 1ypi_ca_cb.pdb -o 1ypi.gro -p 1ypi.top -ff charmm27.ff<br>error: Could not find force field 'charmm27.ff' in current directory, install tree or GMXDATA path.<br>
<br>2) when i used option export GMXLIB=/home/maruthi/1ypi to current directory <br><br>error: atom N not found in buiding block 1ALB while combining tdb and rtp<br> where as there are no N atom in my pdb file<br> <br>3) when i used -ter option, and selected n-terminal none and c terminal none , i got the following error,<br>
WARNING: atom CB is missing in residue ALB 240 in the pdb file<br><br><br>WARNING: atom CA is missing in residue ALB 241 in the pdb file<br><br><br>WARNING: atom CB is missing in residue ALB 242 in the pdb file<br>
<br><br>WARNING: atom CA is missing in residue ALB 243 in the pdb file<br><br><br>WARNING: atom CB is missing in residue ALB 244 in the pdb file<br><br><br>WARNING: atom CA is missing in residue ALB 245 in the pdb file<br>
<br><br>WARNING: atom CB is missing in residue ALB 246 in the pdb file<br><br><br>WARNING: atom CA is missing in residue ALB 247 in the pdb file<br><br><br>WARNING: atom CB is missing in residue ALB 248 in the pdb file<br>
<br>Fatal error:<br>There were 247 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology anyhow, use the option -missing<br>For more information and tips for troubleshooting, please check the GROMACS<br>
<br>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.<br><br><br>Thank you in advance,<br><br>Regards,<br>Mohan<br><br>