Hi,
You will need parameters for your iron - the Amber force fields do not
have parameters for heavy metals, but does come with the Metal Center
Parameter Builder (MCPB) that is well-suited to problems like this.
Check out the MCPB tutorial for an intro:
http://ambermd.org/tutorials/advanced/tutorial20/
Hope this helps,
-Dan
On Fri, Feb 26, 2016 at 6:14 AM, Anna Cebrian Prats
<Anna.Cebrian.uab.cat> wrote:
> Hi,
>
>
> I am working with a protein with 10750 atoms which have a coordinate sphere with Fe (III). There are 5 residues and one -oH group take part of the coordinate sphere.
>
>
> Then, in order to create the prmtop and inpcrd with tleap, I used the following input:
>
>
> source leaprc.ff14SB
> loadoff atomic_Fe.lib
> 3o8Y = loadpdb 3o8y_definitivo.pdb
> loadamberparams frcmod.ionslrcm_cm_tip3p
> loadamberparams frcmod.ionsjc_tip3p
> solvatebox 3o8Y TIP3BOX 10
> check 3o8Y
> charge 3o8Y
> addions 3o8Y NA 0
> savepdb 3o8Y Fe_3o8Y.pdb
> saveamberparm 3o8Y Fe_3o8Y.top Fe_3o8Y.crd
> quit
>
>
> and appear the following error:
>
>
>>Checking Unit.
>>Building topology.
>>Building atom parameters.
>>For atom: .R<FE 674>.A<FE 1> Could not find vdW (or other) parameters for type: FE
>>Parameter file was not saved.
>
>
> The problem is that I want to include a path for Fe(III) - -HO- coordinate sphere
>
> type as follows but for amber. This is possible?
>
>
> PRES FE35 -1.65 ! +1.000 original charge.
>
> GROUP ! P1:673 (ICT) formal= -1.000; NPA= -0.685; diff= +0.315
> ATOM 1OT2 OC2 -0.355 ! orig= -0.670; diff= +0.315 type from CHARMM
> ATOM 1OT1 OC1 -0.670 ! added manually
> ATOM 1C CC1 0.340 ! added manually
>
> GROUP ! P1:367 (IMD) formal= -0.000; NPA= +0.122; diff= +0.122
> ATOM 2NE2 NR21 -0.578 ! orig= -0.700; diff= +0.122 type from CHARMM
>
> GROUP ! P1:372 (IMD) formal= -0.000; NPA= +0.141; diff= +0.141
> ATOM 3NE2 NR22 -0.559 ! orig= -0.700; diff= +0.141 type from CHARMM
>
> GROUP ! P1:550 (IMD) formal= -0.000; NPA= +0.096; diff= +0.096
> ATOM 4NE2 NR23 -0.604 ! orig= -0.700; diff= +0.096 type from CHARMM
>
> GROUP ! P1:554 (ASN) formal= -0.000; NPA= +0.136; diff= +0.136
> ATOM 5OD1 OR24 -0.450 ! Asn554 in lox5, aprox: leave the same as for HSE; original -0.55 (the same as LM&PS 03/14)
> !HSE545 in LOX15 orig= -0.700; diff= +0.136 type from CHARMM
>
> GROUP ! HYDR:1 (HFE) formal= -1.000; NPA= -0.498; diff= +0.502
> ATOM 6O1 OC3 -0.818 ! orig= -1.320; diff= +0.502 type from CHARMM
> ATOM 6H1 HO 0.320 ! added manually
>
> GROUP ! IRON:1 (FE3) formal= +3.000; NPA= +1.687; diff= -1.313
> ATOM 7FE FE6 +1.724 ! NPA charge used ! +0.001 for compensate roundoff error
>
> !This section is copied from FE25; PS 04/14
>
> BOND 7FE 1OT2 7FE 2NE2 7FE 3NE2 7FE 4NE2 ! 1OT2 to 1OT1; PS 04/14
> BOND 7FE 5OD1 7FE 6O1
> ANGLE 1C 1OT2 7FE 1OT2 7FE 3NE2 1OT2 7FE 4NE2
> ANGLE 1OT2 7FE 6O1 2CD2 2NE2 7FE 2CE1 2NE2 7FE
> ANGLE 2NE2 7FE 3NE2 2NE2 7FE 4NE2 2NE2 7FE 5OD1
> ANGLE 2NE2 7FE 6O1 3CD2 3NE2 7FE 3CE1 3NE2 7FE
> ANGLE 3NE2 7FE 4NE2 3NE2 7FE 6O1 4CD2 4NE2 7FE
> ANGLE 4CE1 4NE2 7FE 4NE2 7FE 5OD1 5CG 5OD1 7FE
> ANGLE 5OD1 7FE 1OT2 5OD1 7FE 6O1
> ANGLE 6H1 6O1 7FE
> DIHED 1C 1OT2 7FE 6O1 1CA 1C 1OT2 7FE
> DIHED 1OT1 1C 1OT2 7FE 2HE1 2CE1 2NE2 7FE
> DIHED 2ND1 2CE1 2NE2 7FE 3HE1 3CE1 3NE2 7FE
> DIHED 3ND1 3CE1 3NE2 7FE 4HE1 4CE1 4NE2 7FE
> DIHED 4ND1 4CE1 4NE2 7FE 5CB 5CG 5OD1 7FE
> DIHED 5ND2 5CG 5OD1 7FE 6H1 6O1 7FE 1OT2
> DIHED 7FE 2NE2 2CD2 2CG 7FE 2NE2 2CD2 2HD2
> DIHED 7FE 3NE2 3CD2 3CG 7FE 3NE2 3CD2 3HD2
> DIHED 7FE 4NE2 4CD2 4CG 7FE 4NE2 4CD2 4HD2
> IMPR 2CE1 2CD2 7FE 2NE2 3CD2 3CE1 7FE 3NE2
> IMPR 4CE1 4CD2 7FE 4NE2
>
>
> Thank you in advanced for you help
>
>
> Sincerely,
>
>
> Anna
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Feb 26 2016 - 07:30:08 PST
