On 5/6/16 4:23 AM, Anna Cebrian Prats wrote:
> Hello,
>
> I have another question respect to my system and the HEM group.
>
> The parameters obtained from database of the HEM group presents Fe+2.
>
> If i want to define the protoporphyrin IX FE +3 group, I have to define a new prep and parm file??
It may depend on your purpose. If you think of it, a different charge on
the central atom will mean different charges in the surrounding ones, so
it would be more accurate to reparameterize the charges. But I suspect
many people have gone down this path with simulating porphyrin, so look
around. If you don't need new charges for the protoporphyrin, you
shouldn't need to have a new prep file for it or different parameter
files, unless you felt a specific need to tinker with the atom types
with an advanced understanding.
> How can I indicate that the iron present Fe +3 or Fe +4?
The residue name and probably the atom name should reflect this, plus of
course the charge will need to be adjusted. Especially when you get up
to 4, I naively wonder if some of the ion charge might even need to be
distributed to other atoms, or if reviewers would believe in your
results with the simulation model (I'm not current enough to know).
> Moreover, If I want construct the protoporphyrin IX FE +4 with an oxygen double bonded to the iron. I have to use the MCPB program?
Amber does not differentiate bond order except in the atom type-based
force constants, which are the only thing to adjust if you have
coordinates. The only exception is that in xleap you can up the order of
a bond by clicking on it, but the only effect is within leap, if you use
the add-hydrogens-and-build option. (It's impressive - credit to Chris
Schafmeister - but I suspect is rarely used.)
Bill
>
> Thank you in advanced for your help
>
> Anna
>
>
> ________________________________________
> De: Anna Cebrian Prats <Anna.Cebrian.uab.cat>
> Enviat el: dimarts, 3 de maig de 2016 12:16:18
> Per a: AMBER Mailing List; david.case.rutgers.edu
> Tema: Re: [AMBER] tleap - protein + ligand + heme group
>
> Hi,
>
> I finally solve it!!!! I get the .top and .rst
>
> Otherwise, thank you for your help
>
> Anna
>
> ________________________________________
> De: Anna Cebrian Prats <Anna.Cebrian.uab.cat>
> Enviat el: dimarts, 3 de maig de 2016 11:47:55
> Per a: AMBER Mailing List; david.case.rutgers.edu
> Tema: Re: [AMBER] tleap - protein + ligand + heme group
>
> Hi,
>
> Thank you for you answer Dac.
>
> I tried like this way, and still not saving the .top and .rst
>
> source leaprc.ff14SB
> source leaprc.gaff
> loadamberparams acd-tosco.frcmod
> loadamberprep acd-paper.in
> loadamberparams heme.frcmod
> loadamberprep Heme-all-atom.prep
> loadamberparams frcmod.ionsjc_tip3p
> x = loadpdb 3hs5-def.pdb
> bond x.357.NE2 x.553.FE
> check x
> addions x Na+ 0
> solvatebox x TIP3PBOX 15. 2.2
> check x
> saveamberparm x 3hs5_B.top 3hs5_B.rst
> savepdb x 3hs5_B_leap.pdb
> quit
>
> The error obtain is written below. The only thing that I don't understand is: if in my pdb I don't have a O2 bonded to a FE why is asking for their torsion and angles?
> The frcmod and prep files neither present a O2-Fe bond nor their angles and torsion.
> I added again the files used , might be someone can help me.
>
> I am doing something wrong?
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: NA - FE
> Could not find bond parameter for: O2 - FE
> Building angle parameters.
> Could not find angle parameter: CW - NA - FE
> Could not find angle parameter: H - NA - FE
> Could not find angle parameter: NA - FE - NP
> Could not find angle parameter: NA - FE - NO
> Could not find angle parameter: NA - FE - NP
> Could not find angle parameter: NA - FE - NO
> Could not find angle parameter: NA - FE - O2
> Could not find angle parameter: CR - NA - FE
> Could not find angle parameter: O2 - FE - NP
> Could not find angle parameter: O2 - FE - NO
> Could not find angle parameter: O2 - FE - NP
> Could not find angle parameter: O2 - FE - NO
> Could not find angle parameter: C - O2 - FE
> Building proper torsion parameters.
> ** No torsion terms for CW-NA-FE-NP
> ** No torsion terms for CW-NA-FE-NO
> ** No torsion terms for CW-NA-FE-NP
> ** No torsion terms for CW-NA-FE-NO
> ** No torsion terms for CW-NA-FE-O2
> ** No torsion terms for H-NA-FE-NP
> ** No torsion terms for H-NA-FE-NO
> ** No torsion terms for H-NA-FE-NP
> ** No torsion terms for H-NA-FE-NO
> ** No torsion terms for H-NA-FE-O2
> ** No torsion terms for NA-FE-O2-C
> ** No torsion terms for CR-NA-FE-NP
> ** No torsion terms for CR-NA-FE-NO
> ** No torsion terms for CR-NA-FE-NP
> ** No torsion terms for CR-NA-FE-NO
> ** No torsion terms for CR-NA-FE-O2
> ** No torsion terms for O2-C-O2-FE
> ** No torsion terms for C-O2-FE-NP
> ** No torsion terms for C-O2-FE-NO
> ** No torsion terms for C-O2-FE-NP
> ** No torsion terms for C-O2-FE-NO
> ** No torsion terms for CT-C-O2-FE
> Building improper torsion parameters.
> old PREP-specified impropers:
> <ACD 552>: C14 C16 C15 H20
> <ACD 552>: C15 C13 C14 H19
> <ACD 552>: C11 C13 C12 H16
> <ACD 552>: C12 C10 C11 H15
> <ACD 552>: C8 C10 C9 H12
> <ACD 552>: C9 C7 C8 H11
> <ACD 552>: C5 C7 C6 H8
> <ACD 552>: C6 C4 C5 H7
> <ACD 552>: C2 O1 C1 O2
> <HEM 553>: NA C1A C4A FE
> <HEM 553>: NB C1B C4B FE
> <HEM 553>: NC C1C C4C FE
> <HEM 553>: ND C1D C4D FE
> <HEM 553>: C1A C2A NA CHA
> <HEM 553>: C1B C2B NB CHB
> <HEM 553>: C1C C2C NC CHC
> <HEM 553>: C1D C2D ND CHD
> <HEM 553>: C2A C3A C1A CAA
> <HEM 553>: C2B C3B C1B CMB
> <HEM 553>: C2C C3C C1C CMC
> <HEM 553>: C2D C3D C1D CMD
> <HEM 553>: C3A C4A C2A CMA
> <HEM 553>: C3B C4B C2B CAB
> <HEM 553>: C3C C4C C2C CAC
> <HEM 553>: C3D C4D C2D CAD
> <HEM 553>: C4A NA C3A CHB
> <HEM 553>: C4B NB C3B CHC
> <HEM 553>: C4C NC C3C CHD
> <HEM 553>: C4D ND C3D CHA
> total 1895 improper torsions applied
> 29 improper torsions in old prep form
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
> Parameter file was not saved.
>
>
>
> Thank you in advanced for your help
>
> Sincerely,
>
>
> Anna
>
>
>
>
>
> ________________________________________
> De: David A Case <david.case.rutgers.edu>
> Enviat el: divendres, 29 d'abril de 2016 18:27:28
> Per a: AMBER Mailing List
> Tema: Re: [AMBER] tleap - protein + ligand + heme group
>
> On Fri, Apr 29, 2016, Anna Cebrian Prats wrote:
>> I try to use the prep and frcmod get it from data base ( added in this email), for the group heme (UNIT HEM)
>>
>> For atom: .R<HEM 556>.A<NA 2> Could not find vdW (or other) parameters for type: NP
> Arrgh...somehow the frcmod.hemall file on the web site is out of date.
> Try the one attached here...just has two additional lines at the bottom,
> defining vdW parameters for NP and NO.
>
> Thanks for being patient, and for pointing this out. I'll get the files fixed
> on the web database.
>
> Here is a leap.in file (annotated slightly) that I recently used to construct
> a model that has two Mb-like proteins:
>
> source leaprc.ff14SB
> source leaprc.gaff # need this for my ligand
> loadAmberPrep heme_all.in
> loadAmberParams frcmod.hemall # use the version attached in this email
> CMO = loadMol2 cmo.mol2 # my ligand, which is CO
> SO4 = loadMol2 SO4_ipq_spce.mol2 # sulfate ions also in the simujlations
> loadAmberParams SO4_ipq_spce.frcmod
> loadAmberParams frcmod.spce # I decided to use SPC/E water here
> loadAmberParams frcmod.ionsjc_spce
> WAT=SPC
> HOH=SPC
> x = loadpdb 1bzr_ucnawat.pdb # loading the pdb file
> bond x.93.NE2 x.154.FE # add the bond from the His to Fe of the hem
> bond x.250.NE2 x.311.FE
> bond x.155.C x.154.FE # add bond between Fe and the CO liagnd
> bond x.312.C x.311.FE
> set x box {34.910 31.040 64.730} # I already had waters, you might do
> # something like solvateOct here
> saveamberparm x 1bzr_uc_wet.parm7 1bzr_uc_wet.rst7
> savepdb x 1bzr_uc_wet.pdb
> quit
>
> ...hope this helps...dac
>
>
>
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Received on Fri May 06 2016 - 06:00:06 PDT
