Hi,
I have a template with a potassium ion and I'm trying to use it in my modelling. What I can see from the manual and file code I should use: % in the .ali MK as atom name in the .pdb K as residue name in the .pdb ATOM instead of HETATM in the .pdb
This how ever doesn't work. I have tried to use e.g. zinc ion and that work (z, ZN2, ZN2 resp.).
I would be very great full for any help!
Regards,
Fredrik.
fredrik wrote: > I have a template with a potassium ion and I'm trying to use it in my > modelling. What I can see from the manual and file code I should use: > % in the .ali > MK as atom name in the .pdb > K as residue name in the .pdb > ATOM instead of HETATM in the .pdb > > This how ever doesn't work. I have tried to use e.g. zinc ion and that > work (z, ZN2, ZN2 resp.).
The easiest solution is to treat the ion as a BLK residue. See http://salilab.org/modeller/FAQ.html#16
Ben Webb, Modeller Caretaker
Thanks for the fast reply!
If I would like to do it the hard way, can I do it like below? I.e. will the modelling be correct? (I've done it and it seems to modell correct.)
Would it be correct to add: ------------------------------------------------------- MK 0.0 -0.0870 1.76375 ! potassium ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol ------------------------------------------------------- in the par.lib, par_all22_prot_b5.inp,
------------------------------------------------------- MASS 94 MK 39.10 ! Potassium ion -------------------------------------------------------
------------------------------------------------------- RESI POT 1.00 ! Potassium ion GROUP ATOM MK MK 1.00 PATCHING FIRST NONE LAST NONE ------------------------------------------------------- in the top_ca.lib
------------------------------------------------------- MASS 109 MK 39.10 ! Potassium ion -------------------------------------------------------
------------------------------------------------------- RESI POT 1.00 ! Potassium ion GROUP ATOM MK MK 1.00 PATCHING FIRST NONE LAST NONE ------------------------------------------------------- in the top.lib, top-charmmH.lib
------------------------------------------------------- MASS 134 MK 39.1 -------------------------------------------------------
------------------------------------------------------- RESI POT 1.00000 ATOM MK MK 1.00000 PATC FIRS NONE LAST NONE ------------------------------------------------------- in the top_allh.lib, top_allh-charmmH.lib, top_polh.lib, top_mnss.lib, top_mnch.lib, top_mcwo.lib, top_mccb.lib, top_heav.lib, top_cacb.lib, top_ca3h.lib,
------------------------------------------------------- MASS 93 MK 39.1 -------------------------------------------------------
------------------------------------------------------- RESI POT 1.00000 ATOM MK MK 1.00000 PATC FIRS NONE LAST NONE ------------------------------------------------------- in the top_all22_prot_b5.inp (Guess this would be unnessesary?!)
Would it be correct to change to: ------------------------------------------------------- 104 | POT | k | POT | potassium ion ------------------------------------------------------- in the restyp.lib, restyp_accelrys.lib?
Fredrik.
Modeller Caretaker wrote: > fredrik wrote: > >> I have a template with a potassium ion and I'm trying to use it in my >> modelling. What I can see from the manual and file code I should use: >> % in the .ali >> MK as atom name in the .pdb >> K as residue name in the .pdb >> ATOM instead of HETATM in the .pdb >> >> This how ever doesn't work. I have tried to use e.g. zinc ion and that >> work (z, ZN2, ZN2 resp.). > > > The easiest solution is to treat the ion as a BLK residue. See > http://salilab.org/modeller/FAQ.html#16 > > Ben Webb, Modeller Caretaker
Fredrik wrote: > If I would like to do it the hard way, can I do it like below? I.e. will > the modelling be correct? (I've done it and it seems to modell correct.)
Everything looks OK. However, since the K+ ion is just a point, this won't give you much beyond treating it as a BLK residue (I think the only difference you'll see is that it'll have a defined VDW radius this way, assuming you also alter radii.lib - Modeller doesn't do electrostatics by default, so the charge is ignored).
> in the par.lib, par_all22_prot_b5.inp,
Modeller doesn't use par_all22_prot_b5.inp - that's the original CHARMM file from which par.lib is derived - so there's no point in editing that.
> in the top_ca.lib > in the top.lib, top-charmmH.lib > in the top_allh.lib, top_allh-charmmH.lib, top_polh.lib, > top_mnss.lib, top_mnch.lib, top_mcwo.lib, top_mccb.lib, > top_heav.lib, top_cacb.lib, top_ca3h.lib, > in the top_all22_prot_b5.inp (Guess this would be unnessesary?!)
You probably only need to change top_heav.lib; the other top_*.lib files are only used if you use non-default topologies. There is no need to change the *-charmmH.lib files, as they're not used by Modeller 7 and above (they are the old versions of top.lib, from Modeller 6). top_all22_prot_b5.inp is the original CHARMM file again, so as you suggested, changing it is redundant.
> Would it be correct to change to: > ------------------------------------------------------- > 104 | POT | k | POT | potassium ion > ------------------------------------------------------- > in the restyp.lib, restyp_accelrys.lib?
Looks OK, although you don't need to change restyp_accelrys.lib - that's only used in the commercial version of Modeller.
Ben Webb, Modeller Caretaker
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