Missing residues in ATB downloaded pdb/rtp files

Question

I have downloaded the diglyme molecule from the ATB server (http://atb.uq.edu.au/molecule.py?molid=34570#panel-md) Two files are available: a PDB file and a topology ITP/RTP file. The name of the molecule is 9AZR, and so is called the residue in the topology file. Unfortunately there is not a forum/manual yet from ATB.

I would like to use these to run in GROMACS but I am pretty confused since the 9AZR residue in unknown. $ gmx pdb2gmx -f atb.pdb

... Fatal error: > Residue '9AZR' not found in residue topology database …

Other molecules, respectively 348621 and 705000, will contain UYKS and PEZE as “residue”. None of this is recognized by pdb2gmx from GROMACS. Shall I define them myself? Or shall I specify their value/reference database? Could I find some explanatory material/tutorial on this subject?

I found this previous discussion very useful: Finding parameters for a molecule in various forcefields especially for suggesting LigParGen as a way around: http://zarbi.chem.yale.edu/ligpargen/ but this will work only for limited cases (OPLS-AA) and ultimately I would like to understand what I am getting wrong here, since GROMACS is supposed to be the native FF ATB was meant to.

Thank you for your support

Marco

Answer 1

The error is due that 9AZR is not a standard residue name.

I recommend you to use the web services CHARMM-GUI. In the left menu, go to Input Generator. There you can generate the topology file as well the input files for different molecular dynamics software (including NAMD, GROMACS, etc.)