Dear all,
I converted a PDB file into Mol2 file using Openbabel (H added) and then fixed the bond order number using this command: perl sort_mol2_bonds.pl jz4.mol2 jz4_fix.mol2
When I try to generate the topology file for my ligand molecule using CGenFF server I get the following error message:
"readmol2 warning: atom or bond number too high; skipped molecule..." (Screenshot attached)
I get a different error on SWISSSPARAM for same file as following:
"Failure report: It was necessary to change the name of the atoms numbered" (Screenshot attached)
Could you please shed some light on what exactly could be wrong here to fix the problem?
With this topology file, I wanted to run an MD simulation of the Protein+ligand complex.
Many thanks,
Deepak
http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-tutorial.pdf
Which forcefield you are using and try to download sdf file of ligand alone and then convert it to mol2 format and try to generate topology for respective ligand mol.
Neeraj Kumar The ligand for which I am trying to generate a topology file is 5kDa polyanionic foldamer. We have made energy minimized PDB models of this ligand. The forcefield is MMFFs. Are there any other servers where I could possibly generate a topology file from?
Thanks.
Deepak Deepak Have you tried other servers like PRODRG 2.5 ATB Antechamber for topology generation? And gromacs provide a number of programming scripts for this purpose. you can find them here http://www.gromacs.org/Downloads/User_contributions/Other_software
Regards
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