To the AMBER List members,
I would like to know if anyone could give me an
information about a DNA molecular dynamic procedure.
I am having problems with the molecular dynamic procedure
specified bellow:
5DNB, initial dynamics w/ belly on DNA, model1, 9.0 cut
&cntrl
nmropt = 1,
ntx = 1, irest = 0, ntrx = 1, ntxo
= 1,
ntpr = 100, ntwx = 500, ntwv = 0, ntwe
= 0,
ntf = 2, ntb = 2,
cut = 9.0, nsnb = 10,
ibelly = 0, ntr = 1,
imin = 0,
nrun = 1,
nstlim = 12500,
ndfmin = 0, nscm = 0,
init = 3, t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 100.0,
ig = 71277, heat = 0.0,
ntt = 1,
tautp = 0.2, tauts = 0.2,
vlimit = 15.0,
ntp = 1, pres0 = 1.0, comp = 44.6,
taup = 0.2, npscal = 1,
ntc = 2, tol = 0.00001,
&end
&wt
type='TEMP0', istep1=0, istep2=500,
value1=100.0, value2=300.0,
&end
&wt
type='TEMP0', istep1=500, istep2=12500,
value1=300.0, value2=300.0,
&end
&wt
type='END',
&end
&rst
iat=0,
&end
Hold the DNA fixed
500.0
RES 1 20
END
END
I tried to change some of the key words above but the new
procedures had the same problem: there are variables that
are not in the namelist.
If possible, I would like to have one archive that run
without problems to deal with because I did not find one
yet.
Sorry if my question is not applicable here in this list
but I am starting working with AMBER.
Thank you in advance.
=====
Andrei Leitão
Doutorando em Química Medicinal
Graduante Student in Medicinal Chemistry
NEQUIM - Núcleo de Estudos em Química Medicinal - Brasil
UFMG - Universidade Federal de Minas Gerais
NEQUIM - Medicinal Chemistry Group - Brazil
UFMG - Federal University of Minas Gerais
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Received on Wed Oct 16 2002 - 08:48:10 PDT
