I am running MD simulation using GROMACS for protein-ligand complex. I used all the softwares (swissparam etc.) for ligand topology. I am always getting new and different errors. Can anybody please help me step by step to generate topology and combine it.
Regards,
Faez Khan
Your topology is simply out of order. #include the ligand immediately after the #include statement for the force field, before any [moleculetype] appears. All force field-level directives must precede molecule-level directives. The force field has to be fully known before it can be used!
Also, be careful with generalizations about using various servers. SwissParam is for CHARMM-compatible topologies, ATB for GROMOS, RED or acpype for AMBER, etc. Whatever you do has to be consistent with a single force field.
You have to use acpype or ATB web server to create the gro and top files of the ligand. Then generate the protein files normally using the odb2gmx. After that, add the ligand generated gro file to the protein gro file, and the ligand itp file to the protein top file.
For a more illustrative example see:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html#NoteTopolGen
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html
Dear MelChor
I did the the same using swissparam. but getting following errors.
Fatal error:
Syntax error - File ligand.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
Second question: using ATB server how to compute "Net charge"??
Thanks
Your topology is simply out of order. #include the ligand immediately after the #include statement for the force field, before any [moleculetype] appears. All force field-level directives must precede molecule-level directives. The force field has to be fully known before it can be used!
Also, be careful with generalizations about using various servers. SwissParam is for CHARMM-compatible topologies, ATB for GROMOS, RED or acpype for AMBER, etc. Whatever you do has to be consistent with a single force field.
hi you can use the web-server PRODRG. you can use the application at this link
http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg
Beware the artifacts of raw PRODRG topologies. The FAQ notes that the charges often don't come out right, but I often see people disregard this very clear warning. The outcomes can be quite bad without proper refinement.
http://pubs.acs.org/doi/abs/10.1021/ci100335w
hi
if you have this Fatal error:
Syntax error - File ligand.itp, line 7
Last line read:
'[ types ] '
Invalid order for directive atomtypes
you must repair your itp file in atomtype CB, CR, HMM.... and so on
Invalid order for directive atomtypes: in your itp file the first things must be moleculetype.
Hi
You can use the ACPYPE server. You must put your molecule in mols format and should put your molecule net charge then you will submit it. you must use the molecule name-new.pdb, molecule name.itp and molecule name.gro files to md simulations.
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