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!
/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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Thanks for all your comments,
the use of "#define " seems to be most convenient solution in my case.
Nicolas
--
[ Nicolas SAPAY, Ph.D. ]
University of Calgary, Dept. of Biological Sciences
2500 University drive NW, Calgary AB, T2N 1N4, Canada
Tel: (403) 220-6869
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