[gmx-users] flexiable water - model

[Nilesh Dhumal]

Hello,

I am trying to run a simulation for flexiable water. I use the parameters
from J. Chem. Phys. (2006),124,024503 paper and made floowing changes.

I addes "WAT" as a new residue name in aminoacids.dat

I addred two atom times in ffoplsaa.atp

 opls_1001   15.99940  ; O SPC_fw Water
 opls_1002    1.00800  ; H SPC_fw Water


I added following parameters in ffoplsaa.rtp

[ WAT]
 [ atoms ]
 OWA   opls_1001  -0.82 1
 HWA1  opls_1002   0.41 2
 HWA2  opls_1002   0.41 2

  [ bonds ]
 OWA   HWA1
 OWA   HWA2

I made a spc_fw.itp file.

; Derived from parsing of runfiles/alat.top.orig
 [ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
;1               3               yes             0.5     0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

 [ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_type    mass    charge   ptype          sigma      epsilon
 opls_1001   OWA  8    15.99940     -0.820       A    3.1655e-01  6.503e-01
 opls_1002   HWA  1     1.00800      0.410       A    0.00e+00  0.00e+00

[ bondtypes ]
; i    j  func       b0          kb
 OWA    HWA      1    0.1012   443153.3808 ; J. Chem. Phys. (2006),124,024503


[ angletypes ]
;  i    j    k  func       th0       cth
  HWA     OWA     HWA      1   113.24   317.5656  ; J. Chem. Phys.
(2006),124,024503

[ moleculetype ]
; Name            nrexcl
 WAT             3

[ atoms ]

; nr       type  resnr residue  atom   cgnr     charge       mass  typeB  
 chargeB      massB
1  opls_1001   1    WAT     OWA      1      -0.82
2  opls_1002   1    WAT    HWA1      1       0.41
3  opls_1002   1    WAT    HWA2      1       0.41

[ bonds ]
; i     j       funct
1       2       1
1       3       1


[ angles ]
; i     j       k       funct
2       1       3       1


Finally I made changes in ffoplsaa.itp file

;#include "ffoplsaanb.itp"
;#include "ffoplsaabon.itp"
#include "spc_fw.itp"
#include "spc_fw_mol.itp"

For pdb2gmx

 pdb2gmx -f water.pdb -o water.pdb -p water.top -ter

I get following error

Fatal error:
Atom OWA in residue HOH 1 not found in rtp entry with 3 atoms
             while sorting atoms


WHy is reading HOH residue. In my pdb file I mentioned WAT as residure.

How can I fix this error?

Nilesh