[AMBER-Developers] Re: Atomic radii assignment for WAT molecules

From: MengJuei Hsieh <mengjueh.uci.edu>
Date: Mon, 30 Nov 2009 16:40:36 -0800

This has been in the bugzilla for some period of time at

This can be reproduced with this command in tleap:
    saveamberparm TP3 wat.prmtop wat.inpcrd
And the output prmtop becomes
      1.50000000E+00 8.00000000E-01 1.20000000E+00

In my preliminary test, H2(HW) is recorded to be linked to an HW, which
generates a radius of 1.2, but H1(HW) is recorded to be linked to an OW,
which generates a radius of 0.8.

>From what Dimas said, it should be 1.2 but LEaP's solvate* commands
generate all 0.8 radii for HW.

Here I provide in the attachment a patch to src/leap/src/leap/unitio.c:
After patching, both directly loading WAT and solvate commands produce 1.2
radii for HW.

Mengjuei Hsieh, Molecular Biology & Biochem, Univ. of California Irvine.
On Sat, Nov 28, 2009 at 10:13 AM, Ray Luo <ray.luo.uci.edu> wrote:
> 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 ...
> On Thu, Nov 26, 2009 at 8:43 AM, DIMAS RODRIGUEZ <dimas.uniovi.es> 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) :
>> ..........................................
>>  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...

AMBER-Developers mailing list

Received on Mon Nov 30 2009 - 17:00:02 PST
Custom Search