[gmx-users] flexiable water - model

[Nilesh Dhumal]

I have total 256 water molecules. I am trying to genrate the .top file
from  .pdb so I used pdb2gmx.

How can I genrate the .top file with pdb2gmx for 256 water molecules.

Nilesh

On Tue, April 26, 2011 1:01 pm, Justin A. Lemkul wrote:
>

>
> 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
>
>
> --
> ========================================
>
>
> 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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