[gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.
Rana Rehan Khalid
rrkhalid at umich.edu
Fri Jun 16 00:38:38 CEST 2017
kindly tell me sir how i can i add residue
On Thu, Jun 15, 2017 at 2:04 AM, Rana Rehan Khalid <rrkhalid at umich.edu>
wrote:
> thanks justin
> actually i want to know that how these values of column (atom name, type,
> charge and charge group) we obtain for oxygen bonded with heme fe. is there
> any program through which i find the parameter file for oxygen with heme
> and nitric oxide with heme iron. if i just add the atom name type and
> charge in the bonded type heme fe atoms is it work for me can you tell me
> about any tutorial in which adding residue shows with examples that will be
> very understandable. thanks
>
> On Wed, Jun 14, 2017 at 4:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/14/17 12:25 AM, Rana Rehan Khalid wrote:
>>
>>> Hi
>>> I have read the chapter 5 of manual but i am confuse how can i add
>>> residue
>>> into heme atom of .rtp ff
>>> this is the coordinate due to which error come
>>>
>>> HETATM 1529 O01 HEM 187 3.996 19.101 70.594 0.00
>>> 0.00 O
>>>
>>> kindly guide me how i can make changes in the rtp file and .atp so that
>>> this error remove
>>> here is the heme rtp part of my selected ff where i can add O01 and also
>>> tell me these 4 column and these values and tell me which value i add for
>>> O01 like (FE FE 0.40000 0 )
>>>
>>
>> You should refer back to the manual if the contents of these files are
>> not clear. You're seeking to introduce new parameters for an oxygen-bound
>> form of heme; this may require very complex parametrization work.
>> Modifying an .rtp file is trivial; it's just text. Putting realistic
>> parameters into it is a whole other matter. Check the literature for any
>> existing efforts to avoid duplicated work.
>>
>> -Justin
>>
>> [ HEME ]
>>> [ atoms ]
>>> FE FE 0.40000 0
>>> NA NR -0.10000 0
>>> NB NR -0.10000 0
>>> NC NR -0.10000 0
>>> ND NR -0.10000 0
>>> CHA C -0.10000 1
>>> HHA HC 0.10000 1
>>> C1A C 0.00000 2
>>> C2A C 0.00000 2
>>> C3A C 0.00000 2
>>> C4A C 0.00000 2
>>> CMA CH3 0.00000 3
>>> CAA CH2 0.00000 4
>>> CBA CH2 0.00000 4
>>> CGA C 0.27000 5
>>> O1A OM -0.63500 5
>>> O2A OM -0.63500 5
>>> CHB C -0.10000 6
>>> HHB HC 0.10000 6
>>> C1B C 0.00000 7
>>> C2B C 0.00000 7
>>> C3B C 0.00000 7
>>> C4B C 0.00000 7
>>> CMB CH3 0.00000 8
>>> CAB CR1 0.00000 9
>>> CBB CH2 0.00000 9
>>> CHC C -0.10000 10
>>> HHC HC 0.10000 10
>>> C1C C 0.00000 11
>>> C2C C 0.00000 11
>>> C3C C 0.00000 11
>>> C4C C 0.00000 11
>>> CMC CH3 0.00000 12
>>> CAC CR1 0.00000 13
>>> CBC CH2 0.00000 13
>>> CHD C -0.10000 14
>>> HHD HC 0.10000 14
>>> C1D C 0.00000 15
>>> C2D C 0.00000 15
>>> C3D C 0.00000 15
>>> C4D C 0.00000 15
>>> CMD CH3 0.00000 16
>>> CAD CH2 0.00000 17
>>> CBD CH2 0.00000 17
>>> CGD C 0.27000 18
>>> O1D OM -0.63500 18
>>> O2D OM -0.63500 18
>>>
>>> thanks
>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
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