I am interested in minimising the protein ligand complex by defining
*restraints
for all backbone atoms*. I am also interested in using *harmonic potential* in
my minimization input to conform the minimized atoms to my initial
structure (reference structure (wet.complex.rst7).
Apologies for being naive and not being able to understand AMBER
My query is about the input file that I am using for this . I was wondering
if this is ok or how can I make it more better to get a good minimised
structure.
Minimize
&cntrl
imin=1,
ntx=1,
irest=0,
maxcyc=2000,
ncyc=1000,
ntpr=100,
ntwx=0,
cut=10.0,
ntb=2,
ntp=1,
ntr=1,
ntf=2,
ntc=2,
restraint_wt=10,
restraintmask= ':1-198.CA,C,O,N,H' # total number of aa are 198 and lig
is 199
/
and this is the command that i am using
#!/bin/sh
sander* -O -i* min.in* -o* min.out* -p* wet.complex.prmtop* -c*
wet.complex.rst7* -r* min.rst7 -ref wet.complex.rst7 -inf min.info
I was wondering if it would be right to include ligand in
restraintmask like instead of putting 1-198 will it be ok to use 1-199 and
then ions for restraints.
Thank you in advance
Arooma
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Received on Wed Dec 22 2021 - 13:30:02 PST
