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

[Justin Lemkul]

On 2/4/14, 5:15 AM, Marieke Schor wrote:
> 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.
>

The AMBER force fields parametrize the N- and C-terminal residues individually, 
so unfortunately the normal Gromacs terminal assignment approach cannot be 
applied.  The N- and C-terminal versions of each amino acid are listed as a 
separate .rtp entry, so if you want to add a new one, you have to add it to 
aminoacids.rtp by following 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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