Re: [AMBER] tleap - protein + ligand + heme group

From: Anna Cebrian Prats <Anna.Cebrian.uab.cat>
Date: Tue, 3 May 2016 09:47:55 +0000

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 Tue May 03 2016 - 03:00:06 PDT
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