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

Marieke Schor mschor at ed.ac.uk
Tue Feb 4 11:16:21 CET 2014

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
2) if someone has AMBER99sb-ILDN protonated C-termini itp that would  
be even better.

Thanks a lot,

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

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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