I have generated a .str file from .pdb file using CGenFF server. But whenever I try to convert the .str file to gromacs specific topology using:
python3 cgenff_charmm2gmx_py3_nx2.py JZ4 jz4_clean.mol2 jz4_clean.str charmm36-mar2019.ff
Folllowing error occurs :
This script has been tested with NetworkX 2.3, and 2.4 is buggy.
Please install version 2.3 for best performance:
pip uninstall networkx
pip install networkx==2.3
NOTE 1: Code tested with Python 3.5.2 and 3.7.3. Your version: 3.8.2 (default, Jul 16 2020, 14:00:26)
[GCC 9.3.0]
NOTE 2: Code tested with NetworkX 2.3. Your version: 2.5rc2.dev_20200825190836
NOTE 3: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation:
--Version of CGenFF detected in jz4_clean.str : 4.0
--Version of CGenFF detected in charmm36-mar2019.ff/forcefield.doc : 4.1
WARNING: CGenFF versions are not equivalent!
NOTE 4: To avoid duplicated parameters, do NOT select the 'Include parameters that are already in CGenFF' option when uploading a molecule into CGenFF.
Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (32) and top (0) are unequal
Usually this means the specified residue name does not match between str and mol2 files.
Is there any way to do this conversion in some other software because gromacs is giving one error after other ?
Sidra Ashraf, you can use your pdb file to generate GROMACS topology file using the "gmx pdb2gmx" command.
gmx pdb2gmx -f "input.pdb" -o "output.pdb" (or gro file) -p topol.top (Topology file) -i posre.itp -n index.ndx
Check out the documentation: http://manual.gromacs.org/archive/5.0.4/programs/gmx-pdb2gmx.html
Rajlaxmi Saha i am trying to make topology file for ligand therefore pdb file cannot be used directly to get gro file in gromacs.
The document you suggested says " Note that a .pdb file is nothing more than a file format, and it need not necessarily contain a protein structure. Every kind of molecule for which there is support in the database can be converted. If there is no support in the database, you can add it yourself "
how to add support for ligand in database kindly suggest
What is your ligand? Is it some biomolecule that CHARMM-FF (or other FF) doesn't have requisite force field parameters?
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