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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Received on Fri Feb 26 2016 - 05:30:03 PST
