The question is just simply is it possible via tleap parametrize
protein with ions taken both from given pdb obtaining rough model for
first instance
e.g I have pdb consisted of protein with several ions embedded within
specified bound sites
I found that params for the ions are present within the ff03 thus
creating input :
set default PBradii mbondi2
source leaprc.ff03.r1
source leaprc.gaff
protein = loadpdb my.pdb
addions protein Na+ 0
addions protein Cl- 0
setbox protein centers
solvateBox protein 10.0
check protein
saveamberparm protein protein.parm7 protein.inpcrd
savepdb protein out.pdb
quit
eventually I obtained from tleap
Checking parameters for unit 'protein'.
Checking for bond parameters.
Checking for angle parameters.
check: Errors: 5 Warnings: 18
Checking Unit.
FATAL: Atom .R<CU 898>.A<CU 1> does not have a type.
FATAL: Atom .R<MG 899>.A<MG 1> does not have a type.
FATAL: Atom .R<CA 900>.A<CA 1> does not have a type.
FATAL: Atom .R<CU 901>.A<CU 1> does not have a type.
FATAL: Atom .R<CU 902>.A<CU 1> does not have a type.
Is it possible to add params for the ions for such input?
Thanks!
James
2016-06-29 16:39 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
> Dear Amber users!
>
> My question is related to force-field-based optimization of the
> protein which has several 2+ metal ions (CU CA FE) and MG ions
> embedded within it as cofactors.
> The question is what amber params which will be provided by tleap
> should I use for proper parametrization of the ions embedded within
> the protein fold and how the ions should be named properly within each
> of the models?
>
> Thanks for help!
>
> James
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Received on Thu Jun 30 2016 - 04:00:02 PDT
