Dear Thomas and Dave,
This might be an old issue but you would not believe that I have been
working on and off on this thing since our last communication on 11/12. I am
new to amber so I took that long. Anyways, this problem is that of Hydrogen
in a phosphate ion overlapping with the oxygen. My first mail stating the
problem is attached below for your quick perusal. I followed what Thomas
suggeted (his mail is also here). I added two new atoms types "hx" and "ox".
I borrowed parameters from his 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. However when I saveamberparm prmtop and inpcrd files, it gives me the
error:
Building topology.
Building atom parameters.
For atom: .R<C1P 1>.A<O25 64> Could not find type: ox
Parameter file was not saved.
Is there anything that I am missing? Also I was wondering where do I mention
the radii of these atoms. Frcmod only has the mass. I am sure there is
another file that I need to create (a lib file?) and load that in amber.
Thanks a lot for your help in advance.
Rgds,
Nitin
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.
--
$B&-(BI+I$B'*(B
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Received on Sun Jan 07 2007 - 06:07:31 PST
