[gmx-users] how to fit parameters for terminal residues in amber99sb-ildn?

yoochan yuchan.m at gmail.com
Sat Apr 4 03:54:09 CEST 2015

Dear Sangeun,

Did you try ‘pdb2gmx’ using your structure file?

I checked NME and NHE are in the AMBER99sb-ildn forecefield.

So, if pdb2gmx doesn’t work, you can draw NME and NHE using molecular viewer and then change residue/atom name to NME and NHE.


> On Apr 4, 2015, at 7:01 AM, sang eun jee <sangeunjee at gmail.com> wrote:
> Dear  gromacs users
> Hello. I have question how to decide terminal residue forcefield and put
> them in library?
> I am using AMBER99sb-ildn forcefield in gromacs. Not like gromos or opls
> forcefield, amber forcefield treat termini in its own way and current
> version only works with NH3+ and COO-. I would like to termini as a neutral
> status, NH2 and COOH and would like to modify forcefield to include this
> specific termini data.
> To decide charges and parameters to describe specific termini, is there any
> way to decide parameters based on non-terminal residue database? When I
> looked at NGLY and GLY from animoacids.rtp,  I could not find out specific
> rules.
> Thank you very much.
> Sangeun Jee
> -- 
> Post Doctoral Researcher
> School of Materials Science and Engineering
> Georgia Institute of Technology
> -- 
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