[gmx-users] How to extend Ryckaert-Bellemans parameters?
nsapay at ucalgary.ca
Wed Mar 21 16:48:46 CET 2007
Yang Ye wrote:
> 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!
>> 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.
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Thanks for all your comments,
the use of "#define " seems to be most convenient solution in my case.
[ Nicolas SAPAY, Ph.D. ]
University of Calgary, Dept. of Biological Sciences
2500 University drive NW, Calgary AB, T2N 1N4, Canada
Tel: (403) 220-6869
Fax: (403) 289-9311
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