[gmx-users] Invalid order for directive defaults

Atila Petrosian atila.petrosian at gmail.com
Wed Nov 13 13:06:31 CET 2013


Dear Justin

My cnt is infinite.

I obtained cnt.top by g_x2top and then modified cnt.top to cnt.itp.

For obtaining cnt.top, I used following files:
-----------------------------------------------------------
ffcnt.atp:

CA      12.01100 ;      aromatic C
-----------------------------------------------------------
ffcnt.n2t:

C    CA    0.00    12.011  3    C 0.141   C 0.141   C 0.141
C    CA    0.00    12.011  2    C 0.141   C 0.141
-----------------------------------------------------------
ffcntbon.itp:

[ bondtypes ]
; i	j	func	b0	kb
CA  CA	3	0.1418   47890.0   21.867

[ angletypes ]
; i	j	k	func	th0	cth	ub0	cub
CA	CA	CA	2	120.00	562.20

[ dihedraltypes ]
; i	j	k	l	func	phi0	cp	mult
CA      CA      CA      CA      5  0.00 25.12 0.00 0.00
-----------------------------------------------------------
ffcntnonbon.itp:

[ atomtypes ]
;name	at.num	mass	charge	ptype	sigma	epsi
CA	6	12.01100	0.00	A	0.385   0.4396
-----------------------------------------------------------
In cnt.itp file, angle section of file is as follows:

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    2     1     8     1
    2     1   287     1
    8     1   287     1
    1     2     3     1
    1     2    10     1
    3     2    10     1
    2     3   289     1
    2     3   406     1
  289     3   406     1
    5     4    17     1
    5     4   320     1
   17     4   320     1
    4     5     6     1
.
.
.
.
.
.

I saw system.gro file by VMD, there are all angles defined above in
[angle] directive.



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