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.*
--
========================================
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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