[AMBER] Ligand Minimization with Simulated Annealing

From: Julian Zachmann <FrankJulian.Zachmann.uab.cat>
Date: Mon, 6 Jun 2011 16:24:51 +0200

Dear Users.

I am trying to run Simulated Annealing to minimize ligands that I have
downloaded from a database. "Normal" minimization was not successful as it
brought me only to the closest minima but still the ligand conformation is
I have no restraint and I want to run them in vacuum.

But I got the mistake:
Could not find cntrl namelist

What did I do wrong?
This is the first time I am running SA in Amber so I am thankful for any
other advises concerning the input file.

Best Regards,

This is the input file that I used:

    nstlim=15000, ntt=3, gamma_ln=1000.0
    cut=18.0, ntb=0, vlimit=20
    ntc=1, dielc=10,

 &wt type='TEMP0', istep1=0,istep2=1000,
 &wt type='TEMP0', istep1=1001, istep2=3000,
 &wt type='TEMP0', istep1=3001, istep2=15000,
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Received on Mon Jun 06 2011 - 07:30:03 PDT
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