[gmx-users] flexiable water - model

[Mark Abraham]

On 4/27/2011 1:29 AM, Nilesh Dhumal wrote:
> 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

This is a wrong approach. You should model your .itp file on the 
existing standard water .itp files. They are designed so that you can 
simply #include them in other topologies from the right places. Yours 
cannot be used in this way, because you have erroneously used a 
[defaults] directive (which can only appear once in a topology). You 
should #include the main force field files, then #include a 
properly-formed spc_fw.itp for the atom, bond and molecule types, then 
specify your [molecules], as Justin said.

Mark

>   [ 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
>
>
>
>
>