[gmx-users] TIP3P water box

[Justin A. Lemkul]

kecy_wu at sina.com wrote:
>  Hello,I want to  use spc216.gro and apply the tip3p.itp parameters, but 
> it would make a mistake for the pre-processor "grompp" ,it said can't 
> find HW atomtypes, the force file which I used is "ffG43a1.itp". my 
> tip3p.itp file is as follows: 

HW isn't a valid atom type for ffG43a1.  See the .atp file for what is.  What 
you probably want is H, not HW.

-Justin

> 
>  /[ moleculetype ]
> ; molname nrexcl
> SOL  2/
> 
> /[ atoms ]
> ; id at type res nr  residu name at name  cg nr charge
> #ifdef _FF_OPLS
> 1     opls_111  1       SOL              OW             1       -0.834
> 2     opls_112  1       SOL             HW1             1        0.417
> 3     opls_112  1       SOL             HW2             1        0.417
> #endif
> #ifdef _FF_CHARMM
> 1       OT      1       SOL              OW             1       -0.834
> 2       HT      1       SOL             HW1             1        0.417
> 3       HT      1       SOL             HW2             1        0.417
> #endif
> #ifdef _FF_GROMACS
> 1       OWT3    1       SOL              OW             1       -0.834
> 2       HW      1       SOL             HW1             1        0.417
> 3       HW      1       SOL             HW2             1        0.417
> #endif
> #ifdef _FF_GROMOS96
> 1       OWT3    1       SOL              OW             1       -0.834
> 2       HW      1       SOL             HW1             1        0.417
> 3       HW      1       SOL             HW2             1        0.417
> #endif/
> 
> /#ifdef FLEXIBLE
> [ bonds ]
> ; i j funct length force.c.
> 1 2 1 0.09572 502416.0 0.09572 502416.0
> 1 3 1 0.09572 502416.0 0.09572 502416.0
>  /
> 
> /[ angles ]
> ; i j k funct angle force.c.
> 2 1 3 1 104.52 628.02 104.52 628.02 /
> 
> /#else
> [ settles ]
> ; i j funct length
> 1 1 0.09572 0.15139/
> 
> /[ exclusions ]
> 1 2 3
> 2 1 3
> 3 1 2
> #endif/
> 
> the version of the gromacs is 4.0.5.
> 
>  
> 
> Thank you for all your help !
> 
>  
> 

-- 
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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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