AMBER Archive (2009)

Subject: [AMBER] Strange contacts with water molecules

From: Jordan MONNET (monnet.jordan_at_free.fr)
Date: Mon Jun 08 2009 - 16:39:26 CDT

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 



--
Jordan MONNET (3rd grade student)
Bachelor in Biology & Computer science
University of Paris Diderot (Paris VII)
Phone: +336 20 70 24 93

http://monnet.jordan.free.fr/

" The most exciting phrase to hear in science, the one that heralds  
new discoveries, is not 'Eureka!' but 'That's funny...' "
Isaac Asimov

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