You need to model your O's. Probably good to read up on O2 modeling in
Amber.
Maybe you need to make O2 not be part of the heme? Is it bonded?
If it's bonded, read my previous mail on the subject closely for
instructions.
Bill
On 7/2/17 9:11 PM, Rana Rehan Khalid wrote:
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-FE-ND-*
> +--- With Sp0 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> Created a new atom named: O01 within residue: .R<HEM 187>
> Created a new atom named: O02 within residue: .R<HEM 187>
> ERROR: Comparing atoms
> .R<HEM 187>.A<ND 55>,
> .R<HEM 187>.A<NC 39>,
> .R<HEM 187>.A<NB 23>, and
> .R<HEM 187>.A<NA 2>
> to atoms
> .R<HEM 187>.A<ND 55>,
> .R<HEM 187>.A<NC 39>,
> .R<HEM 187>.A<O1 74>, and
> .R<HEM 187>.A<NA 2>
> This error may be due to faulty Connection atoms.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 142
> !FATAL: Message: Atom named O1 from HEM did not match !
> !
> !ABORTING.
>
> On Sun, Jul 2, 2017 at 11:57 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> wrote:
>
>> Hi everyone
>> I am trying to load pdb file that consist of heme---O2 through xleap i
>> use these commands
>> source leaprc.protein.ff14SB
>> source leaprc.gaff
>> loadamberparams argn.frcmod
>> loadamberprep argn.in
>> loadpdb oxyhem.pdb
>>
>> xleap close
>> and these error show on terminal window after closing xleap
>> +--- Sp0 probably means a new atom type is involved
>> +--- which needs to be added via addAtomTypes
>> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
>> +---Tried to superimpose torsions for: *-NC-FE-*
>> +--- With Sp2 - Sp0
>> +--- Sp0 probably means a new atom type is involved
>> +--- which needs to be added via addAtomTypes
>> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
>> +---Tried to superimpose torsions for: *-FE-ND-*
>> +--- With Sp0 - Sp0
>> +--- Sp0 probably means a new atom type is involved
>> +--- which needs to be added via addAtomTypes
>> !FATAL ERROR----------------------------------------
>> !FATAL: In file [chirality.c], line 142
>> !FATAL: Message: Atom named O1 from HEM did not match !
>> !
>> !ABORTING.
>>
>>
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Received on Sun Jul 02 2017 - 21:30:03 PDT
