Are you sure you are using the results of the minimizations as your
starting coords?
What were initial/final energies of the minimizations? (paste, please)
What is your mdin file?
Bill
On 11/19/17 11:16 PM, Carlos Romero wrote:
> Hi dear AMBER users:
>
> I try to make a MD for a complex (602 residues), but when I heat it, it
> does not work, appears the following:
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
> I understand that it is because of some atoms are overlapping,
> I analyzed coordinates from crystallographic structure and I found many
> overlapped coordinates, but they do not disappear with minimization.
> I started with the following min.in
> &cntrl
> imin = 1,
> maxcyc = 2500,
> ncyc = 1000,
> ntb = 1,
> ntr = 0,
> cut = 8
>
> /
> I did three consecutive minimizations and problem persist.
> I would appreciate any suggestion.
>
> Thanks in advance.
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Received on Mon Nov 20 2017 - 00:30:05 PST
