[gmx-users] creating topology using g_x2top

[Justin A. Lemkul]

sreelakshmi ramesh wrote:
> Dear all ,
>             I want to simulate a double walled nano tube in spc water i 
> had made the pdb file now if i use g_x2top for creating the topology 
> file it gives me the following error .
> 
> Now if i run * g_x2top -f out.pdb -o out.top -ff oplsaa*
> it gives the following error
> 
> *Can not find forcefield for atom OW-5432 with 2 bonds
> Can not find forcefield for atom OW-5435 with 2 bonds
> Can not find forcefield for atom OW-5438 with 2 bonds
> Can not find forcefield for atom OW-5441 with 2 bonds
> Can not find forcefield for atom OW-5444 with 2 bonds
> Can not find forcefield for atom OW-5447 with 2 bonds
> Can not find forcefield for atom OW-5450 with 2 bonds
> 
> 

Presumably you have water in your starting structure.  Don't run g_x2top on 
configurations with multiple molecules.  Run the command on your CNT and nothing 
else, then proceed to solvate and simply #include the .itp file for your desired 
water model in the .top.

-Justin

> looking forward for your  suggestions,
> Thanks in advance,
> sree.*
> 

-- 
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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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