well, just tried to freeze ligand using
restraint_wt=50.0, restraintmask=':lig'
and it does not work at all!
Frozen or restrained atoms:
ibelly = 0, ntr = 0
and in the MD, it still moves ;-)
So how could the mask be modified?
Il giorno gio 24 nov 2022 alle ore 17:10 Enrico Martinez
<jmsstarlight.gmail.com> ha scritto:
>
> Ciao Gustavo,
> actually I would like to apply it rather than using name of the
> residues (lig) together with the atom type instead of the number of
> atom
> This trick would help me to use the same mask on different ligands
> with the same type..
>
> e.g.an example when I apply additional restrains of the whole ligand
>
> '(.CA,CA,N,O & !:WAT) | :lig'
>
> would it be something like
> '(.CA,CA,N,O & !:WAT) | :lig.C1'
>
> ??
>
> Il giorno gio 24 nov 2022 alle ore 17:04 Gustavo Seabra
> <gustavo.seabra.gmail.com> ha scritto:
> >
> > Is it possible to just add the atom number (9281) to the mask?
> >
> > --
> > Gustavo Seabra.
> > ________________________________
> > From: Enrico Martinez via AMBER <amber.ambermd.org>
> > Sent: Thursday, November 24, 2022 10:51:11 AM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: [AMBER] Applying position restraint on ligand
> >
> > Dear Amber Users,
> >
> > Currently I am performing equilibration of my protein-ligand system
> > using the following amber mask used to freeze all backbone atoms of
> > protein excluding water residues (containing O atom)
> >
> > restraintmask='(.CA,CA,N,O & !:WAT)'
> >
> > Using this selection, I would like to add selected atom of the ligand
> > (residue "lig") e.g. to apply position restraints on the atom C1.
> > Here is the PDB format of the ligand present in the same model:
> >
> > ATOM 9275 N lig 608 -7.093 -20.714 4.036 1.00 0.00
> > ATOM 9276 N1 lig 608 -6.438 -17.078 3.587 1.00 0.00
> > ATOM 9277 N2 lig 608 -8.410 -24.956 0.057 1.00 0.00
> > ATOM 9278 N3 lig 608 -6.296 -24.226 -0.519 1.00 0.00
> > ATOM 9279 N4 lig 608 -9.281 -23.257 11.747 1.00 0.00
> > ATOM 9280 C lig 608 -4.815 -25.159 7.597 1.00 0.00
> > ATOM 9281 C1 lig 608 -5.456 -24.863 8.800 1.00 0.00
> > ATOM 9282 C2 lig 608 -6.465 -23.902 8.829 1.00 0.00
> > ATOM 9283 C3 lig 608 -6.793 -23.211 7.658 1.00 0.00
> > ATOM 9284 C4 lig 608 -6.145 -23.506 6.451 1.00 0.00
> > ATOM 9285 C5 lig 608 -5.159 -24.496 6.422 1.00 0.00
> > ATOM 9286 C6 lig 608 -6.493 -22.779 5.220 1.00 0.00
> > ATOM 9287 C7 lig 608 -6.641 -21.287 5.234 1.00 0.00
> > ATOM 9288 C8 lig 608 -6.682 -23.457 4.077 1.00 0.00
> > ATOM 9289 C9 lig 608 -7.285 -21.470 2.886 1.00 0.00
> > ATOM 9290 C10 lig 608 -7.052 -22.793 2.837 1.00 0.00
> > ATOM 9291 C11 lig 608 -7.305 -19.306 4.000 1.00 0.00
> > ATOM 9292 C12 lig 608 -8.576 -18.774 4.226 1.00 0.00
> > ATOM 9293 C13 lig 608 -6.272 -18.418 3.711 1.00 0.00
> > ATOM 9294 C14 lig 608 -8.763 -17.395 4.159 1.00 0.00
> > ATOM 9295 C15 lig 608 -7.679 -16.600 3.824 1.00 0.00
> > ATOM 9296 C16 lig 608 -7.165 -23.504 1.566 1.00 0.00
> > ATOM 9297 C17 lig 608 -8.393 -24.307 1.260 1.00 0.00
> > ATOM 9298 C18 lig 608 -6.185 -23.519 0.646 1.00 0.00
> > ATOM 9299 C19 lig 608 -7.391 -24.975 -0.850 1.00 0.00
> > ATOM 9300 C20 lig 608 -8.007 -22.375 9.811 1.00 0.00
> > ATOM 9301 C21 lig 608 -9.283 -22.478 10.593 1.00 0.00
> > ATOM 9302 C22 lig 608 -10.498 -21.874 10.307 1.00 0.00
> > ATOM 9303 C23 lig 608 -10.458 -23.196 12.328 1.00 0.00
> > ATOM 9304 C24 lig 608 -10.887 -20.992 9.174 1.00 0.00
> > ATOM 9305 O lig 608 -6.405 -20.658 6.265 1.00 0.00
> > ATOM 9306 O1 lig 608 -9.335 -24.385 2.045 1.00 0.00
> > ATOM 9307 O2 lig 608 -7.445 -25.622 -1.888 1.00 0.00
> > ATOM 9308 O3 lig 608 -7.163 -23.529 9.947 1.00 0.00
> > ATOM 9309 Cl lig 608 -3.583 -26.361 7.561 1.00 0.00
> > ATOM 9310 S lig 608 -11.642 -22.255 11.530 1.00 0.00
> >
> >
> > Could you please suggest to me how the restraint mask indicated above
> > could be modified in order to freeze ligands at one point of the atom
> > C1?
> > Many thanks in advance!
> > Cheers,
> > Enrico
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Nov 25 2022 - 01:00:02 PST
