Hi,
You have to explain your system in more details. For example, are the ions
coordinated or free; If latter the leaprc.water.tip3p (ambertool16) would be
nice for Ca and Mg. However, the most probable case is that your ions are
coordinated and need to be parameterized. Copper ion should be definitively
processed. MCPB.py tool is a nice toll to do it.
Cheers
Zoran
-----Original Message-----
From: James Starlight
Sent: Thursday, June 30, 2016 12:44 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Structural refinement of the protein complexed
withmetalo-ions
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 - 05:30:04 PDT
