[gmx-users] flexiable water - model

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> I have total 256 water molecules. I am trying to genrate the .top file
> from  .pdb so I used pdb2gmx.
> 

pdb2gmx is only really useful for building topologies for linear molecules built 
from repeat building blocks, not for systems of individual molecules.

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

With a text editor:

#include "ffoplsaa.itp"

#include "spc_fw.itp"

[ system ]
water

[ molecules ]
WAT 	256


-Justin

> 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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>>
> 
> 
> 

-- 
========================================

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

========================================