[gmx-users] More ATP errors

Raj Badhan r.k.badhan at stud.man.ac.uk
Mon Dec 8 12:00:01 CET 2003

Dear Sirs,
After hours of trying to get my simulation to run with ATP as a 
ligand I have almost given up all hope.
ATP is the ligand within my protein.
I can run an em protocol with the protein alone and with the ligand 
alone, but not with both together, as MDRUN always crashes.
I have checked for bad contacts and there are none.
Any suggestions? I am running this on the windows ported version 
of gromacs, and below is my EM.MDP file.
Has anyone been able to use ATP as a ligand and got the 
simulations to work? If so, I would appreciate any 
ideas/suggestions on how they got their simulation to work.

title = FWS
cpp = c:\gromacs\bin\cpp.exe
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 400
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Energy minimizing stuff
emtol = 1000.0
emstep = 0.01
Raj Badhan
Postgraduate researcher
School of Pharmacy and Pharmacetical Science
The University of Manchester
Manchester, UK.

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