Try this:
1. Paste this at the place of my_ions.itp to replace it.
[ moleculetype ]
NA+ 1
[ atoms ]
1 amber99_31 1 NA+ NA+ 1 1 22.99000
[ moleculetype ]
CL- 1
[ atoms ]
1 amber99_30 1 CL- CL- 1 -1 35.45000
2. Replace "Ions 1" with
Na+ 6
Cl- 2
Good luck.
Regards,
Yang Ye
D. Ensign wrote:
from 1
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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?
Yang Ye
As requested, kind person, here is my ions topology include file:
; BEGIN
[ moleculetype ]
; Name nrexcl
Ions 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB
massB
1 amber99_31 1 Na Na 1 1 22.99 ; qtot 1
2 amber99_31 2 Na Na 2 1 22.99 ; qtot 2
3 amber99_31 3 Na Na 3 1 22.99 ; qtot 1
4 amber99_31 4 Na Na 4 1 22.99 ; qtot 2
5 amber99_31 5 Na Na 5 1 22.99 ; qtot 2
6 amber99_31 6 Na Na 6 1 22.99 ; qtot 2
7 amber99_30 7 Cl Cl 7 -1 35.45 ; qtot 1
8 amber99_30 8 Cl Cl 8 -1 35.45 ; qtot -2
; END
For your comparison enjoyment, here is the .itp that I used as a guide for the
template
above. This .itp was generated after I ran genion on a previous, less
interesting system,
then ran pdb2gmx over again which built the .itp below. Unfortunately, running
pdb2gmx in
the present case would be a bit of a pain, since I'm using GAFF parameters for
my
inhibitor and the cofactor, and I want to mess with the ffamber99 files as
little as
possible.
; BEGIN -- template itp file with ions that works, whereas the one above doesn't
[ moleculetype ]
; Name nrexcl
Protein_B 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB
massB
1 amber99_31 1 Na Na 1 1 22.99 ; qtot 1
2 amber99_31 2 Na Na 2 1 22.99 ; qtot 2
3 amber99_30 3 Cl Cl 3 -1 35.45 ; qtot 1
4 amber99_30 4 Cl Cl 4 -1 35.45 ; qtot 0
5 amber99_30 5 Cl Cl 5 -1 35.45 ; qtot -1
6 amber99_30 6 Cl Cl 6 -1 35.45 ; qtot -2
; Include Position restraint file
#ifdef POSRES
#include "posre_B.itp"
#endif
; END -- template itp file that works.
I'm really wondering if having the ions after the solvent is what's messing
this up -- in
the original case, the ions come after the solvent, whereas in the second case
(the
template case) the ions come before the solvent in the gro and in the top.
Which means
I'll be spending a portion of the afternoon writing a Perl script! Woohoo!
Dan Ensign
Stanford University
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