[gmx-users] Vacuum simulations

Anton Feenstra feenstra at chem.vu.nl
Tue Feb 10 08:45:04 CET 2004

Martina Bertsch, PhD wrote:

> Greetings.
> I would like to refine Autodock3 results of docking a nonpeptidic 
> indolic ligand to a membrane receptor model. Because it is 
> computationally expensive to simulate receptors in the membrane (the 
> 5-ns position restrained MD to relax the POPC takes me ~ 20 days), I 
> would like to use MD or simulated annealing in vacuum for some 
> intermediate refinement steps.
> I can generate the protein gro file suitable for vacuum simulations by 
> selecting the ffG43b1 parameter set in pdb2gmx. But, how do I generate 
> the ligand gro and itp consistent with this forcefield? I tried using 
> the ffgmx version of the ligand (as created in PRODRG) and editing the 
> vacuum ff to include the atomtypes, but somehow that does not seem like 
> the right thing to do.

No, you cannot mix atom types from different forcefields. So, instead
you must choose appropriate 'ff43a1' atom types for your ProDrg generated
'ffgmx' topology. Also, you will need to select appropriate 'ff43a1' types
for all bonds, angles, dihedrals and impropers (that is the way it must be
done in the Gromos forcefield). IIRC, I posted a script to the list (or
the contributions page), that will replace atom numbers in your .itp/.top
file by labels that include the atom type, as well as another script that
does the opposite. Having atom type info in stead of atom numbers makes
choosing bond-, angle- and dihedral-types so much easier. If you cannot
find these scripts, please ask me.

> Which energy groups do I specify for monitoring to estimate the 
> receptor-ligand binding energy: protein and drg or protein_drg?

protein and drg


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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