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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