> > so what could be your recommendation ? is there a way to adjust for the
> > close contacts ?
>
> Don't be afraid to experiment. A short (say 100 step) minimization using
> sander with ntmin=3 and some constraints (ntr=1) on non-hydrogen atoms
> should tell you a lot.
I also try a first minimization with electrostatics turned off; if
there are overlapping atoms of opposite charge, charge wins over vdw and
the opposite charges may/will collapse leading to failure.
<notchpeak1 1029> more
../cheatham-group4/DNA/research/G-DNA/3ibk/inputs/min_noelec.in
production
&cntrl
imin = 1, maxcyc = 300, ncyc = 300,
ntb = 2, ntp = 1,
cut = 9.0,
iwrap = 1,
lastist = 10000000,
lastrst = 10000000,
nmropt = 1,
&end
&wt
type = 'ELEC', value1 = 0.0,
&end
&wt
type = 'END',
&end
DISANG=inputs/restraints.in
LISTOUT=POUT
<notchpeak1 1030> more ../cheatham-group4/DNA/research/G-DNA/3ibk/inputs/restraints.in
&rst iat = 0, &end
Good luck --tec3
\-/ Professor Thomas E. Cheatham, III
-/- Department of Medicinal Chemistry, College of Pharmacy
/-\
\-/ tec3.utah.edu
http://www.chpc.utah.edu/~cheatham
-/- SKH-4914 (801) 587-9652
/-\
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 24 2026 - 14:00:03 PDT
