[AMBER] Query regarding minimization in AMBER 20

From: Arooma Maryam <maryam16arooma.gmail.com>
Date: Wed, 22 Dec 2021 16:08:57 -0500

I am interested in minimising the protein ligand complex by defining
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

















  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


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

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Received on Wed Dec 22 2021 - 13:30:02 PST
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