I am not sure assigning vdw parameters without serious rationale is the
best approach. What happened was that the bond was the one holding H
from being attracted to O but the H does not have a vdw radii (much like
in TIP3P water).
This is not a problem in MD so long as you use rigid bonds for those
connecting H atoms (with SHAKE), which is required if you intend to use
dt=2fs. But in MIN, since you did not invoke this, the H can potentially
get over the small energy barrier. Potential solutions for this, rather
than playing with the parameters which could have unexpected effect, are
1) set small dxm (oddly, dxm will be retired in amber8) or 2) invoke
SHAKE (and observe that minimization never converge). Sounds horrible
(particularly for inexperienced), but actually it is really not bad at
all.
yong
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of L Jin
> Sent: Wednesday, February 18, 2004 1:57 PM
> To: amber.scripps.edu
> Subject: Re: AMBER: Close contact warnings
>
>
> Thank you Bill. Is it possible to modify some VDW parms to
> avoid the HO and OS
> or some other atoms to sit on top of each other? Or what
> other methods to
> consider? Thanks.
>
> Lan
>
>
>
>
> Quoting Bill Ross <ross.cgl.ucsf.edu>:
>
> > > The type of H54 is HO 'hydroxyl group' within parm99.
> > > And in my molecule it is attached to the oxygen which is
> > > part of the sulfate group, -SO3H. I have
> > > introduced the atom type for the S atom. And O41 is OS in
> parm99 too. The
> > > positions of H54 and O41 are like this R-O41-SO3H54. Both
> of the parms of
> > H54
> > > and O41 are from Parm99. Do I need to modify the VDW parm? Thanks
> >
> > HO has no vdw. Given that hydroxyls in the Cornell et al. ff
> > are modeled as vdw-less HO's within the radius of the OH, perhaps
> > it is worth considering adding a sulfate O type with an even larger
> > radius, perhaps the same as OW or larger. Here are the radii of the
> > oxygen types:
> >
> > O 1.6612 0.2100 OPLS
> > O2 1.6612 0.2100 OPLS
> > OW 1.7683 0.1520 TIP3P water model
> > OH 1.7210 0.2104 OPLS
> > OS 1.6837 0.1700 OPLS ether
> >
> > Such an approach would keep in the spirit of the Cornell et al. ff;
> > alternatively one could think of using an H type with a non-0 vdw.
> >
> > Bill Ross
> >
> --------------------------------------------------------------
> ---------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
>
>
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Feb 18 2004 - 19:53:01 PST
