[Apbs-users] Questions regarding setup of a simulation with iAPBS and NAMD

[Alexander V. <ale...@we...>]

Hello everybody,

we are trying to simulate lipids in implicit solvent. Later on a peptide will be added as well. We want to use the CHARMM forcefield and so far we could compile a NAMD version with iAPBS. But I still have several questions regarding the setup of the simulation:

1. Since I'm not very familiar with APBS I'm using the default values and only specify cglen, fglen and temp. Are there any other keywords that I should consider adding?

2. What are good values for cglen and fglen? The size of my box?

3. I have to create a PQR file in order to run the simulation. Unfortunately it seems that PDB2PQR can't handle lipids so I have to find some other way to create this file. If I understand correctly the PQR file is just a PDB file with additional information on atom radius and charge. Can I take the charges from the CHARMM topology files for that?

4. How do I calculate the atom radii?

5. Are pH and salt concentration treated somehow and if yes how can I specify that?

I'll probably have even more questions as things progress but that are the most pressing ones right now. Thanks for any help,

Alexander
________________________________________________________________
Neu: WEB.DE Doppel-FLAT mit Internet-Flatrate + Telefon-Flatrate
für nur 19,99 Euro/mtl.!* http://produkte.web.de/go/02/