Dear Amber users,
I have been trying to simulate a molecule that has a hydrogen in a
phosphate ion. The problem is that of Hydrogen overlapping with the oxygen.
Picture is sthg like this:
O2-----P----O1---H1
|
|
C
Now if I use amber atomtype (instead of gaff), in the first step of
minimization itself, H1 almost overlaps with O2 (distance being 0.001 Ang)
while still being bonded to O1.
I posted this on the amber archive and there were a few suggestions but none
of them worked out. The reason is that type 'ho' has zero vDW radius so it
can overlap with O2.
Following one of the suggestions by Thomas I added two new atoms types "hx"
and "ox". I borrowed parameters from that mail and the remaning parameters
were taken from standard ff for "ho" and "oh". I created a new frcmod file:
***
remark goes here
MASS
hx 1.008 0.135 Hydroxyl group
ox 16.00 0.465 Oxygen in hydroxyl group
BOND
ox-hx 525.0 1.480
hx-ox 553.0 0.946
ox-p5 321.2 1.625
ANGLE
ox-p-ox 45.0 101.31
hx-ox-p 45.0 106.31
ox-p5-o 43.8 115.03
os-p5-ox 44.9 102.37
p5-ox-hx 55.9 110.14
DIHE
IMPROPER
NONBON
******
My prepin file now has these lines (ho and oh were changed to hx and ox):
67 O25 ox S 66 65 62 1.500 109.510 60.035 -0.79030
68 H26 hx E 67 66 65 1.000 109.499 59.987 0.42421
When I load the leaprc.ff99 leaprc.gaff (these have not been touched), the
prepin and frcmod file, the molecule gets loaded fine. I 'check' and its
fine. I also created a new library to add these atoms types.
But still the things are not working out, although H1 does not overlap with
O2 anymore. There is only a single molecule containing the phosphate ion in
a water box and as soon as the simulation starts the molecule moves out of
the waterbox and waterbox gets divided into four boxes with a gap between
these boxes.
This whole thing is driving me crazy. I have tried all the ideas and its
beginning to get frustrating.
Are the new force-fields coming out soon that will handle this problem of
'ho' having zero vDW radius being handled? Is there anyother thing that I
can possiby try.
Thanks a lot for your help in advance.
Rgds,
Nitin
- Show quoted text -
On 11/12/06, Thomas Steinbrecher <steinbrt.scripps.edu> wrote:
>
> Dear Nitin,
>
> in a simulation of a protein containing a protonated ADP molecule I ran
> into similar troubles as you before. My solution to this was to build a
> frcmod file that contained to new atom types to describe a P-O-H
> structure.
>
> It contained parameters modelled partly from the ones Heather Carlson used
> in Meagher et al. J Comp Chem, 24, 1016-1025.
>
> In my opinion adding just a vdW parameters for H is not going to be
> enough, I am pretty sure you will need an angle parameter too. This is
> because hydrogens are small (vdW-wise) but in a phosphate setup, they
> might have large positive partial charges next to large negative ones on
> the oxygens.
>
> In my simulation I added types OX and HX, with these bond/angle parms:
>
> ox-hx 525.0 1.480
> hx-ox 553.0 0.946
>
> ox-p-ox 45.0 101.31
> hx-ox-p 45.0 106.31
>
> potentials were taken by analogy from similar fragments, geometries from
> an energyminimized h2po4 molecule. Suprisingly, no dihedral potential was
> necessary, because the potential for rotation around an h-o-p-o dihedral
> with these parameters is reasonably accurate when compared to a HF6-31G*
> QM calculation.
>
> You can experiment a little with vdWparameters for the H, but I would
> assume that you can keep the zero ones from ho.
>
> This worked well for me, but I never did in-depth testing on how realistic
>
> this potential model is.
>
> > h1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963
>
> vdW-radius is the first number, potential well depth the other.
>
>
> Regards,
>
> Dr. Thomas Steinbrecher
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> San Diego CA 92037, USA
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NITIN WROTE:
Dear Amber users,
I am having a strange problem during my simultion. For one of my lipids, I
have a hydrogen (say H1) connected to an Oxygen (say O1). O1 is in turn
connected to Phosphorus (P). Also connected to P is another oxygen (say O2)
that is negatively charged. Picture is sthg like this:
O2-----P----O1---H1
|
|
C
Now if I use amber atomtype (instead of gaff), in the first step of
minimization itself, H1 almost overlaps with O2 (distance being 0.001 Ang)
while still being bonded to O1.
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Received on Sun Jan 07 2007 - 06:07:48 PST
