[gmx-users] How to extend Ryckaert-Bellemans parameters?

Yang Ye leafyoung81-group at yahoo.com
Wed Mar 21 03:29:44 CET 2007

Mark Abraham wrote:
> Nicolas Sapay wrote:
>> As it is not possible to do that in the ffxxxbon.itp file, I was sure 
>> it was the same thing in all other files. But it works perfectly with 
>> my .top files... Thanks!
> /headscratch
> It should work in the .itp file too, since your .top file is just 
> including that... The trick here is that if you use the same atom set 
> and function type, it will over-write any previous occurrence.
To overcome this trick (or "trap"), you may just use #define 
A_B_DIHEDRAL n x y z in ffxxxbon.itp and A B A_B_DIHEDRAL in ffxxx.rtp 
under the [ dihedral ] section of your residue. You may place multiple 
entries for atoms A and B. They will be preserved after pdb2gmx and 
copied to your top file.

Stanford's ffamber port uses this trick. You may check their ffamber99 
set of files.
> Mark
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