[gmx-users] protein simulation w/ urea + water

[Justin A. Lemkul]

E. Nihal Korkmaz wrote:
> Dear all,
> 
> I am trying to simulate a protein in urea solution. I used /*genbox -cp 
> protein_in_box.gro -cs urea+h2o.gro -o out.gro -p topology*/ but the 
> resulting topology doesn't contain any information on urea nor the atoms 
> of urea. I also tried adding ureas on the protein with */-ci 
> urea_single.gro -nmol some_number/* option of genbox, that didn't give 
> me the correct topology either.
> 
> How should i create the correct topology?
> 

By hand.  genbox only writes information related to SOL and is hard-coded to do 
so.  You'll have to #include an appropriate urea topology and update the 
[molecules] section accordingly.

-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

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