Dariush Mohammadyani wrote:
Dear user,
When I am using:
genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro
to add water in a coarse grained system, after running mdrun I am
getting "Syntax error" and it shows maybe the distances are so close or
there are some clashes.
I've never heard of mdrun throwing a syntax error. Can you please copy and
paste the complete error message from your terminal?
Do you know how can I figure it out?
Or actually if we have some clashes in system how we can correct them?
Better energy minimization typically solves bad atomic clashes.
-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
========================================
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