AMBER Archive (2009)

Subject: [AMBER] problems with EP of TIP4PEW

From: rebeca (rebeca_at_mmb.pcb.ub.es)
Date: Wed Jun 03 2009 - 10:43:58 CDT

Hi,
I am trying to use the model TIP4PEW for water. I am using this script:

setenv AMBERHOME /SOFT/amber10
$AMBERHOME/exe/tleap
source leaprc.ff99
loadamberparams parm99EP.dat
loadoff ions08.lib
loadoff tip4pewbox.off
loadamberparams frcmod.ionsjc_tip4pew
loadoff big_cnt.lib
addions mol Na+ 30 Cl- 30
WAT = T4E
loadamberparams frcmod.tip4pew
solvatebox mol TIP4PEWBOX 8.0
saveamberparm mol solvated.top solvated.crd
quit

I think that there is a problem with the lonely pair EP, since I obtain
warnings of the type:

WARNING: There is a bond of 0.149967 angstroms between:
------- .R<WAT 3398>.A<EPW 4> and .R<WAT 3398>.A<O 1>
WARNING: There is a bond of 0.150217 angstroms between:
------- .R<WAT 3399>.A<EPW 4> and .R<WAT 3399>.A<O 1>

Besides, the leap.log file also shows that the EP is not recognized:

> loadamberparams parm99EP.dat
Loading parameters: ./parm99EP.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.23/06/99
(UNKNOWN ATOM TYPE: HZ)
(UNKNOWN ATOM TYPE: NY)
(UNKNOWN ATOM TYPE: IM)
(UNKNOWN ATOM TYPE: Li)
(UNKNOWN ATOM TYPE: IP)
(UNKNOWN ATOM TYPE: K)
(UNKNOWN ATOM TYPE: Rb)
(UNKNOWN ATOM TYPE: Cs)
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: IB)
(UNKNOWN ATOM TYPE: EP)

Could anyone help me to find out why EP is not recognized if it is defined
in parm99EP?

Thank you very much for your help. 

-- 
Rebeca García Fandiño
Molecular Modelling and Bioinformatics Group
Institut de Reçerca Biomèdica 
Parc Cientific de Barcelona
08028 Barcelona

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