[gmx-users] endcapping

[w.j.schravendijk at students.pharm.uu.nl]

To go back on the endcapping business again, pdb2gmx kept changing
my amide-endgroup to a carboxyl, so I decided to edit the ffgmx-c.tdb
and added the entry:

[ CONH2 ]
[ replace ]
C       C       C       12.011  0.53
O       O       OA      15.9994 -0.548
[ add ]
1       2       C       CA      O
        NT      N       14.0067 -0.83
2       3       NT      C       CA
        H       H       1.008   0.415

This more or less works fine, only two problems emerge:

(1) The amide isn't completely planar (which it should be)
CA <-> C <-> NH2 lie in the same plane, but the O is flipped 30 degrees.
This is not a very big problem, but is there something I could do about
it?

(2) grompp gives the error:
Warning 1 [file "2mlti.top", line 1404]:
  No default Angle types, using zeroes

Should this worry me?

Greetings, Pim

  -=-=  =-== =--=-- --  == =-== -- -= =--  --==--==  =-=-==

"He's coming. I must go to meet him."

== Excerpt from 'Nosferatu, a Symphony of Terror' (1922) ==