Dear all,
I am trying to look at the water on a model but the H2O molecules
looks pretty weird... You will find a pdb as attachment to have a
look, you can notice that the H2O molecules have some odd positions/
contacts around DNA. My question is : where does this problem come
from? Anyway, it does not seem to interfere on the global energy which
looks correct
Here is my sander input file :
&cntrl
imin = 0, ntx = 7, irest = 1,
timlim = 999999, ig = 99775, ibelly = 0, ntr = 0,
ntb = 2,
dielc = 1, cut = 9.0, scnb = 2.0, scee = 1.2,
ntc = 2, tol = 0.0005, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 1, tautp = 0.2,
ntp = 1, pres0 = 1.0, taup = 0.2,
nstlim = 1000000, dt = 0.002, ndfmin = 6, ntcm = 1, nscm = 100,
ntpr = 50, ntwx = 500,
&end
Here is my ptraj input file :
trajin model19.mdcrd
center :1-4
image familiar
trajout traj.pdb pdb
go
I run on amber10 with TIP3PBOX.
Thank you
Received on Tue Jun 09 2009 - 01:14:03 PDT
