[gmx-users] AMBER99sb-ILDN - protonated C-terminus

[Marieke Schor]

Hi, I would like to test the effect of low pH on the stability of my  
protein hexamer. For the neutral pH case I used the AMBER99sb-ILDN  
forcefield but this appears not to have parameters to describe a  
protonated C-terminus. I can only find one paper that uses  
AMBER99sb-ILDN with protonated C-termini and this study used NAMD to  
run the simulations. So far, I am having a hard time figuring out how  
to convert these to GROMACS AMBER99sb-ILDN parameters. Could anyone  
help me with either
1) how to convert these AMBER/NAMD parameters to a GROMACS compatible itp file
or
2) if someone has AMBER99sb-ILDN protonated C-termini itp that would  
be even better.

Thanks a lot,
Marieke


-- 
Dr. Marieke Schor
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ


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