D. Ensign wrote:
Greetings.
I'm having a lovely time with my old pal grompp, except for the grumpiness
after replacing
eight water molecules with ions in my system and discovering -- to my
astonishment -- the
following message:
"Atoms in the .top are not numbered consecutively from 1"
Well, this is interesting, seeing as how it's preventing me from advancing, so
is
garnering all my attention. So I have a look at my topol.top, and I discover the
following:
; BEGIN
; Topology for human aldose reductase with NAD+ and inhibitor
; Include force field
#include "ffamber99.itp"
; Include protein topology
#include "haldr.itp"
; Include inhibitor topology
#include "inh1.itp"
; Include NAD+ topology
#include "nad.itp"
; Include water topology
#include "ffamber_tip3p.itp"
#include "my_ions.itp"
[ system ]
hAldR with inhibitor in water
[ molecules ]
;molecule name number
AldoseReductase 1
Inhibitor1 1
NAD 1
SOL 27048
;SOL 27056
Ions 1
;END
Now, the odd thing is, when I comment out references to the Ions molecule and
my_ions.itp,
and remove the ions from the .gro file, everything works just fine! (Well, it
works fine
enough.) That's odd because I haven't treated the ion atoms in my_ions.itp any
differently than I treated the atoms in Inhibitor1 or in NAD, other than
they're after
the water.
paste your my_ions.itp here?
What might be going on here?
Frustrated enough to throw things, but not hard enough to spill my beer,
Dan Ensign
Stanford University
Yang Ye
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