[gmx-users] flexiable water - model

[Justin A. Lemkul]

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
> 
>  [ 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?
> 

If I recall, pdb2gmx does some internal translations to standardize water 
nomenclature.  In reality, you don't need pdb2gmx at all - you've already shown 
that you're created a topology for the water model.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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