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:
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MK 0.0 -0.0870 1.76375 ! potassium
! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol
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in the par.lib, par_all22_prot_b5.inp,
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MASS 94 MK 39.10 ! Potassium ion
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RESI POT 1.00 ! Potassium ion
GROUP
ATOM MK MK 1.00
PATCHING FIRST NONE LAST NONE
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in the top_ca.lib
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MASS 109 MK 39.10 ! Potassium ion
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RESI POT 1.00 ! Potassium ion
GROUP
ATOM MK MK 1.00
PATCHING FIRST NONE LAST NONE
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in the top.lib, top-charmmH.lib
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MASS 134 MK 39.1
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RESI POT 1.00000
ATOM MK MK 1.00000
PATC FIRS NONE LAST NONE
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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,
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MASS 93 MK 39.1
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RESI POT 1.00000
ATOM MK MK 1.00000
PATC FIRS NONE LAST NONE
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in the top_all22_prot_b5.inp (Guess this would be unnessesary?!)
Would it be correct to change to:
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104 | POT | k | POT | potassium ion
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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.).