AMBER Archive (2009)

Subject: Re: [AMBER] Atomic radii assignment for WAT molecules

From: Ray Luo (ray.luo_at_uci.edu)
Date: Sat Nov 28 2009 - 12:13:42 CST

Dimas,

I just noticed the same thing on Wed. I think there is a bug in leap
when the radii for water got set up for the modified bondi radii. We are
looking into this ...

Thanks a lot for reporting!

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

DIMAS SUAREZ RODRIGUEZ wrote:
> Dear Amber Users & Developers,
>
> I am doing some PB calc on systems containing a few TIP3P water molecules using the PBSA module.
> I noticed that the default atomic radii used in the PB calculations for the water H atoms seem to
> be different as shown by PBSA (npbverb= 1) :
>
> NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI
> ..........................................
> 2559 WAT O OW -0.834000 0.000000 0.000000 1.500000 1.500000
> 2560 WAT H1 HW 0.417000 0.000000 0.000000 0.800000 0.800000
> 2561 WAT H2 HW 0.417000 0.000000 0.000000 1.200000 1.200000
>
> These should be modified Bondi radii. The radii values are taken from the parm file
> as generated by tLEaP. If I generate a pqr file using the ambpdb utility, both H atoms
> have a "1.2" radii (i.e., ambpdb does not read the radii from the parm file). I guess that
> the correct value should be 1.2 for the two water H atoms unless there is something
> I am missing here...
>
> Best regards,
>
> Dimas
>
> --------------------------------------------------------------
> Dimas Suarez
> Dpto Quimica Fisica y Analitica
> Universidad de Oviedo
> Julian Claveria 8. 33006. Oviedo. Spain
> Phone: +34-985103689 / 985458019
> Fax: +34-985103125
> http://www.uniovi.es/mrq
> --------------------------------------------------------------
>
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>

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