[gmx-users] forcefield for free (neutral) amino acids

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 29 02:58:52 CEST 2009

FyD wrote:
> Dear chun feng,
>> I am not a user of GROMACS, but I hope someone who's working on  
>> protein dynamics can do me a favor here. I am desperately searching  
>> for a forcefield for free and neutral amino acids. But it seems that 
>>  the forcefields such as amber and opls only parametrizes amino acids  
>> in peptides (without OH and H) and terminal amino acids on peptides.
> Yes
>> I know there has to be some forcefield already developed for popular 
>>  molecules like amino acids, anyone please point me the way! Thanks a  
>> million!
> You could derive your own force field for such amino-acids. You can 
> derive RESP and ESP charges for any molecule or molecular fragment 
> containing chemical elements up to Bromine using the R.E.D. tools. See 
> http://q4md-forcefieldtools.org/

The "Generalized AMBER Force Field" and the AMBER utility program 
antechamber is probably also suited to the task.


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