3
$\begingroup$

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

$\endgroup$
1
$\begingroup$

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.)

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.