AMBER Archive (2009)

Subject: [AMBER] Atomic radii assignment for WAT molecules

From: DIMAS SUAREZ RODRIGUEZ (dimas_at_uniovi.es)
Date: Thu Nov 26 2009 - 10:43:33 CST

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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