http://archive.ambermd.org/201706/0457.html
On 7/2/17 9:27 PM, Rana Rehan Khalid wrote:
> the mail you sent me today?? sir
>
>
> On Mon, Jul 3, 2017 at 12:14 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> 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.
>>>>
>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jul 02 2017 - 22:30:02 PDT
