This looks ok with a quick glance, what does the output file say about the
restraints?
Including the ligand or not depends on what you are trying to do in the
simulation.
On Wed, Dec 22, 2021, 4:09 PM Arooma Maryam <maryam16arooma.gmail.com>
wrote:
> 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 - 14:30:02 PST
