First of all, thank you for your answer.
I am using Amber 9, and the input file is the following:
First minimization
&cntrl
imin = 1,
maxcyc = 3500,
ncyc = 1500,
ntb = 1,
ntr = 0,
cut = 15
/
Did I miss something?
I built the initial structure with the utility packmol. I don't know
other methods in order to set the initial system, because, if I use
the solvatebox command of tleap with my box of PG molecules, I obtain
a box which is too large with a huge number of water molecules (>
190,000).
The system is neutral, I am sure, and parameters are correct. PG
charges are computed with respgen starting from a computation of ESP
with Gaussian 03, using b3lyp/6-311+g(d,p).
Now I try to set the simulation with ntp=1, since I missed it.
Thank you again!
Tommaso
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Received on Tue Jan 25 2011 - 09:00:05 PST
