Dear all,
I am writing you because I tried to parametrize a ligand using xleap. I
parametrized a ligand in a TIP3PBOX with 1 Cl- atom (so as to neutralize the
net charge). During the parametrization stage everything seems work well. At
the end I obtained the ligand.prmtop, ligand.inpcrd, and ligand.pdb files.
First of all I checked the generated fiels using vmd, and everything seems ok.
After that I tried to minimize the ligand using Amber11, I used one processor
and the command line:
sander -i minimization.in -o minimization.out -p prova.prmtop -c prova.inpcrd
-ref prova.inpcrd -r mini_restrt.
But Amber almost immediately crashed with this error message:
Segmentation fault.
Herein the minimization.in file that I used:
Minimization with cartesian restraints
&cntrl
imin=1, maxcyc=10000,
ntmin=1,
ncyc=2000,
ntpr=100,
ntr=1,
restraint_wt=1.5,
restraintmask=':5HE'
/
&ewald
nfft1=64,
nfft2=64,
nfft3=64,
/
attached the minimization.mdout, the mdinfo files
I also tried to perform a minimization of 1 step, and Amber wrote the output,
without any visible problems, but just putting 2 steps of minimization the
system crashed again.
can you help me?
--
Agostino Bruno, PhD
Dipartimento Farmceutico
Universita' degli Studi di Parma
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Received on Wed Mar 28 2012 - 09:00:03 PDT
