GROMACS Full MD Setup failure


#1

Hi - I’m very new to molecular dynamics in general and don’t know what’s going wrong or how to fix what’s going wrong in my GROMACS Full MD Setup. I’m getting the errors below:

2.- Running fixSideChainsFromPDBText Service…
Service Failure.
Workflow Stopped, see program log files.

and in the log files it all seems fine until…

saveAmberParm mol 2_153245009905519.pdb-amber.top 2_153245009905519.pdb-amber.crd
Checking Unit.
WARNING: The unperturbed charge of the unit: 12.000000 is not zero.
FATAL: Atom .R.A does not have a type.

Anybody have any suggestions?


#2

Hi Aaron,

this error is related to the phosphorilated residues (SER, THR) appearing in your structure. These residues are not in the standard force field (in this case Amber99SB*). It is not an easy problem to solve for an automatic platform like MDWeb.

First of all I’m sorry to tell you that MDWeb is not able to work with modified residues (covalently bonded residues) in GROMACS. You can do it in AMBER though, but it requires a number of steps:

You should rename these residues in the PDB file to distinguish them from the standard ones: from SER to SEP and from THR to THP. You should also change the ATOM tag for the HETATM tag. Then MDWeb will be able to recognise them as ligands, and will offer you the possibility to use the parameters coming from the Manchester AMBER parameter database: http://research.bmh.manchester.ac.uk/bryce/amber

One more thing is to rename the atom names in the PDB file to match those in the parameter files (P01 to PS, O01 to OPA, O02 to OPB and O03 to OPC, please see https://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_sep.lib) or just use the ligand checking utility from MDWeb (http://mmb.irbbarcelona.org/MDWeb/help.php?id=checkingLig) to match them.

And still one last thing. I think your structure has a phosphorylated serine in the N-terminal. As the parameters available are for the phospho-serine (not N-terminal phospho-serine), the structure will not be properly prepared with MDWeb. Instead, you can just add a new capping residue or just remove the first phospho-serine (if you know it is not crucial for the protein).

Hope this helps! Thanks for using our tool!


#3

Hi Adam,
Thanks for the explanation - it was very helpful!
I renamed the residues, changed to the HETATM tag, used the ligand checking utility to match the ligand parameter files, added a couple more residues to the N-terminal cap, and switched rotamers on a few residues with major steric clashes. Everything looks to be running well on an Amber Full MD Setup.
Thanks for making the tools more accessible for newcomers!