Hello;
I'm trying to generate different conformers of small peptides using
Amber11. These peptides are also protonated at various sites. When proton
is located at oxygen system blows up. I've red every relevant problems
occured previously and possible solution. I try different starting
structure but it give same problem. Later, writing coordinates on every
step, I visualize the problem also. Proton attached to oxygen clashed with
near N or O atoms. Temperature increased dramatically, the molecule loose
its calm motion and finally gives an error. Here is my input parameter file:
&cntrl
irest=0, ntx=1,
imin=0,
nstlim=20000000, dt =
0.001,
ntwx = 5000, ntwe = 5000, ntwr = -5000, ntpr =
5000,
ntb = 0, ntc = 2, ntf = 2, ntt=3, gamma_ln =
3,
temp0 = 10.0, tautp =
0.4,
cut=999.0, vlimit=21, nmropt=1,
ig=-1
/
&ewald
eedmeth=5,
/
#
#Simple simulated annealing
algorithm:
#
#from steps 0 to 10000: heat the system to
1000K
#from steps 10001-20000000: equilibrium in
1000K
&wt type='TEMP0',
istep1=0,istep2=10000,value1=10.,
value2=1000.,
/
&wt type='TEMP0',
istep1=10001,istep2=20000000,value1=1000.,
value2=1000.,
/
&wt type='TAUTP',
istep1=0,istep2=10000,value1=0.2,
value2=0.3,
/
&wt type='TAUTP',
istep1=10001,istep2=20000000,value1=4.0,
value2=4.0,
/
&wt type='END'
/
Thank you for your attention
Seckin
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Received on Fri May 03 2013 - 04:00:02 PDT
