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

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 21 00:04:46 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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