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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
